I soon realized as I was even asking that this question is pretty loaded and requires a lot of understanding of the terms being used. The answer seeks to define what these three things are, how they work, and where the function of these three tend NOT to overlap (but also, where they do), since if they overlapped to complete congruence, there would be no difference between them. However, I assume that they are different, otherwise if one could reduce the function of the Holy Spirit to either intuition or reasoning skills, in my opinion you would be denying that the Holy Spirit truly is the Spirit of God. And I also assume that Intuition is "different" than reasoning skills because most would describe Intuition as something outside the realm of reasoning, but used to make decisions nonetheless. In all honesty, I actually don't believe that Intuition is different or more special than reasoning skills, but more on that later.
The conflict of the function of these three elements has developed over time as I come to a greater awareness and confusion of the methods in which I make decisions, especially as a person who has often asked for the guidance of the Holy Spirit, and wondering often times if I truly am listening to the Holy Spirit, or if I am simply exhibiting sophisticated reasoning/intuition in the name of the Holy Spirit. I have also been told in the past that I have very little "intuition" (though a Myers-Briggs test will say otherwise), and that I need to increase my intuitive abilities. However many definitions of intuition make intuitive based decision making seem quite magical or metaphysical. It's not that I can't believe in things that are outside today's level of scientific understanding, however how can someone tell me that I need to "increase my intuitive abilities", when intuition across the board seems to be defined as something innate and unconscious. It seems to me that "training" or "practicing" something that by definition is meant to be unconscious would render that very ability or practice as having lost its base definition. In THAT perspective, either Intuition is not truly unconscious and metaphysical in the way it is popularly believed, or you can't train for it because it IS unconscious and metaphysical in the way people typically describe it (though descriptions still vary even among people who do believe in the "magicalness" of intuition). Obviously, there has been very little psychological research in this area.
Again, definitions of intuition vary, however in general the consensus seems to be:
3. The act or faculty of knowing or sensing without the use of rational processes; immediate cognition.
4. Knowledge gained by the use of this faculty; a perceptive insight.
5. A sense of something not evident or deducible; an impression.
I will not spend a great deal of time critiquing and breaking down these definitions, however I will make the blanket statement that these definitions are quite vague, and still don't definitively express what intuition is except by comparing it to other things we are more familiar with such as emotion (instinctive feeling), immediate understanding, sensing, immediate cognition (aka immediate reasoning), perceptive insight (a redundant phrase), an impression (synonymous in ways to "assumption", i.e. "I get the impression you are angry", which would be a loose conclusion based on expressive cues from the other person via facial expressions, tone of voice, context, etc. but nonetheless an assumption without a definitive confession from the other person.).
In my own experience of making decisions I notice that I base decisions either primarily on emotions, or logical/analytical reasoning, and often a combination of the two depending on which ought to take precedence. People often think emotions should be disregarded when making decisions because of their inherently irrational nature--a raging boyfriend deciding to kill his girlfriend made his decision based on his intense anger, and it is clear to most people that making a decision such as this was irresponsible in the least because humanity in general has categorized an act such as this to be unacceptable due to the immense pain it causes to innocent people. To a lesser degree, a person who becomes angry at their friend "unfriends" them on facebook--also a ridiculous decision that was still based on an emotion that lead to irrational behavior. However people often overlook the great utility emotion can play in the decision making process.
For example, when deciding where to go for my undergraduate studies, I listed my three options: Going to TCU all 4 years, Going to ACU all 4 years, Going to a junior/community college 2 years and moving on to another school of choice afterwards. I listed the pro's and con's for each, and even weighted each pro and con on a scale of 1-10 based on which pro's and con's were more or less of a priority to me. For example, the "pro", proximity to home, would rank a "2" for priority while the pro "rave reviews of the school from alumni" would rank close to around an "8". I would then score the pro and con columns for each option, and subtract the score for "con" from the "pro" column, producing the end score for each option. While the "winning" option by this method turned out to be going to a community college first for 2 years, I took a long look at my lists and my math, and "knew in my heart", on an emotional level, that I wanted to attend ACU all 4 years. The idea of going to this school, the perception that I envisioned more life-changing experiences and opportunities compared to going to a community college, and perceiving that I would not have these experiences otherwise all prompted what one might call an "emotion" of positivity toward this decision. I knew this decision would make me happy in a way that would be very important, and I was right. Some might call this "intuition", however my "intuitive" decision was still very well reasoned. After mapping out a pro and con list and trying to reason objectively where I should go, in the end I made my decision based on what I thought would make me truly happy, and though I may not have been fully aware of my reasoning of what would truly make me happy, I can say looking back that deep down I wanted a college experience that was in a sense more monastic and focused. I didn't want to be surrounded by people who just wanted to party. I wanted to be surrounded by people that had a focused spiritual walk and could help guide me on mine. I wanted to be surrounded by faculty members that also did this. I wanted something meaningful. And I knew ACU exhibited these qualities over my other options based on the perception I formulated unconsciously from input about the school from alumni and perusing the school's website. While I realized it at the time or not, I was picking up details about the schools I had considered based on sensory perception (from what I saw, heard, or read), and formulated in my mind, however accurate or inaccurate I might have been, a holistic perception and impression of these schools I had considered based on the information I found. Because of this, ACU probably held a higher favor in my mind even prior to having written out the extensive weighted pro and con scoring measurement, but my attempt at objectively mapping out a reasonable list at least confirmed for me what it was I truly wanted. This is an example of where emotions can take precedence in the decision making process, and can be utilized in the process of reasoning.
A more overt example of emotions becoming a vital tool for decision making would be an experience I had with a friend of mine. This example can be generalized for me, as it is certainly not the first and only time I have experienced this, and I imagine it is a similar experience for many others. I once had a friend who I connected with on an intellectual and spiritual level. Also, we typically spend our time with people we like, and I can say, we did like each other. However, and I will be vague for most of this so as not to give away identity, I found at a point the friendship became a great strain to me. When I was around this person after awhile, I often experienced a low level sense of anxiety, frustration, and discomfort. A lot of this had to do with the way my friend had handled her own stresses, disappointments, and problems in a way I did not see as fruitful to her, and I perceived her emotional expression as one that sought to bring others down with her. While she did not consciously mean harm to others, her behaviors in a sense could be seen as harmful to others. For me, after a time I did discontinue regularly engaging in the relationship. However at first, I came to the understanding that when one experiences negative emotions of this nature in a friendship, it typically means that this person's boundaries were in some way being breached. I reasoned that because negativity can breed more negativity, and I did not believe I was strong enough to combat this with my own sense of positivity, in order to regain a sense of control over myself I needed to create a new boundary specifically modifying the amount of time I spent with this friend so that when she was being negative I would have more "emotional energy" to remain positive. It is a reasonable decision to make, however prompted by emotional cues nonetheless. So while one would not have considered this irrational, it was a decision based on an understanding of what the messages my irrational experience was trying to send me; "This is uncomfortable, do something!!"
It seems to me that if you can slow down your mind for a minute or two in these moments in which you typically make an "intuitive" decision, I am of the belief that you may find the only difference between intuition and reasoning is that intuition involves reasoning that you have not made yourself aware of, and awareness is somewhat a choice. For all the definitions of Intuition as outlined above, all of these fall into either a category of reasoning on an analytical level (just really really fast, based on past experiences, or based on stimuli in your surroundings), or on an emotional level (and I have given two examples already on how it's possible to "reason on an emotional level", for lack of better terms, or in other words utilize emotions for sophisticated decision making rather than reactive behaviors). I feel it is important to understand this further, but I will save that for another post. I emphasize important because as I have been doing a lot of research on moral cognition and development, I find that while it seems harmless to believe something is right or wrong based on an "intuitive", "gut-reactive" sense of right and wrong, then you may lead yourself to believing in a morality that has a very soggy foundation. Especially when assuming a "magical" sense of intuition, rather than intuition in my opinion comes from a complex an unconscious system of reasoning, one is likely to dangerously think that this magical intuition should take precedence over clear reasoning. Sometimes, this is probably not okay. But, again, more on that some other time.
Again, I am at fault for digressing. The base-line importance of defining these elements of decision making (Holy Spirit vs. Intuition vs. Conscious reasoning) is to understand what "voices" I am listening to, and when I ask for the guidance of the Holy Spirit, how do I know that what I am "listening" to is the Holy Spirit? And if it's not, how does one "tap into" that method of decision making? One could say that a deep relationship with God consisting of regular honest prayer with God and a devotion to reading scripture would lend one more perceptive to the message of the Spirit of God, thereby allowing us to make decisions and live our lives in line with the message of the Holy Spirit. To immerse yourself in a certain practice will increase neurons that are dedicated to that practice. It could be as simple as learning a new hobby, or taking a language class. Whatever you are dedicating your time to, you are dedicating neural development to, and whatever you commit neural development to, you will begin to see the world through this lens as your less prioritized neurons begin to prune out. So a person who dedicates their time to devotionals of scripture, prayer, and worship may be given the lens to see the world in a light that this worldview offers. Maybe that is how the Holy Spirit works in the human body/mind/spirit, and this is totally legitimate. Maybe it's important to take the "magical" aspect out of the Holy Spirit, because our God is not a God of magic, and our God may have sought fit to relate to his creatures in a way that we, through science, can comprehend through Psychology and Biology. I think my only personal conflict is seeing how this is truly different from cognitive reasoning. A Christian is typically taught that the Holy Spirit dwells within us from the time that we ask Jesus into our hearts, and are baptized with "the fire" of the Holy Spirit to also dwell within us. In theory, this was not the case for pre-pentecost Jews and Gentiles. The Holy Spirit worked in people, supposedly, in select times throughout Old Testament scripture, and not as a Spirit that dwelled in the people constantly. So, I do see a problem in deducing that the Holy Spirit is manifest in our decision making by the very gift of reasoning and intuition, since I assume reasoning and intuition were things that existed pre-pentecost. In other words, would not an Old Testament Jew who devoted themselves to scripture, worship, and prayer be as inclined to be guided in their decision-making processes in the same way that Christians today call the guidance of the Holy Spirit, if you were to define the roll of the Holy Spirit in decision making as outline above?