How do we know what God's rules are?

This topic has always been a confusing one for me. As a teacher I am often asked 'How can we prove God is real?' My usual answer is that we can't but also, how can we prove that God doesn't exist? I find it hard to get some atheist pupils to understand that once you have experienced God's love and direction in your life it is hard not to believe. But when I am asked by some pupils how I know, as a Christian, what God's rules are I stumble because of two reasons:
1) The answer is obviously that the Bible is like the 'rule book' given to us by God through people in different times and places. This I believe to be part of the truth, but I have issues with the Bible as a complete piece of scripture. I will expand on this below
2) I am inclined to think, that although the Bible was God-breathed, that is, inspired by God (I do not, and have never, considered that God dictated the Bible word by word - again I will expand on this later) and is therefore very important, that God's word and direction through prayer should be considered as showing God's rules. If I need guidance, I pray, as I have been taught and advised by 'older' Christians in the past, and then I listen. It might take me to a place in the Bible, it may be that God answers through another person, or it may be that God answers in His silence. Either way when I think I have an answer, I pray about it again for reassurance. I think that sometimes people get too caught up in relying on the Bible and forgetting that God is alive and can be addressed personally. As far as I am concerned...that is what God wants, a living relationship with His people, not one based solely in the past.

Issues with the Bible as a piece of scripture
I am not going to pull the Bible apart here, as I believe that it is a very important document and as I have said above, I rely on it in many areas of my life.
My problem comes when I think of how the Bible as we know it today, was put together and how some books were included and some were left out by two Councils of men who decided what was 'Godly' and what was not. I am sure that they had stringent rules of what to look for and what not to look for and I am hopeful that there was a lot of prayer involved in the decisions that were finally made. However, a part of me worries that an important part may have been left out or that the men that were a part of the council had an agenda in what they chose to include, consciously or subconsciously.

Obviously, these doubts say more about me than they do about anything but they are there nonetheless. For example, I believe that Paul was a godly man who gave good advice, but it has always worried me that much of the Roman Catholic (amongst others) doctrine about leadership in the church, that is men can lead, women can't, is based on him and essentially his opinion. After all, he is just one man who, whether he meant to or not, wrote from his context. It is doubtful that he considered his words to have such exacting longevity and they would still be being applied today in a totally different time, place and culture. Or that his letters would make up a majority of the New Testament.

My second point about the Bible follows from the previous point. It is that someone, sometime decided to close the book; decided that enough had been written about God and Jesus. When they did this they were stopping God's word in a moment in history. They were leaving the application of those words in the early part of the first century and, for those who believe that the Bible is the infallible word of God to be taken as written, condemning them to try and fit the advice for a particular context into theirs.

*Please do not misunderstand me, I am not suggesting that the Bible is outdated and simply a history book, the point I am trying to make is that it should be open to the changing contexts in which it finds itself. Simply because God is fluid. Therefore, returning to the women in leadership argument, I think Christians should be aware of the context in which Paul was writing when he said that women should not be teachers, should be silent in church etc because there are a plethora of reasons that he may have said it, (including the fact that he may have actually meant women forever, in every context - I am open to that). The thing that concerns me most about religion as opposed to faith is that people do not question, they are told what to believe and what certain passages mean, blind acceptance is never good. I believe that there instead should be a culture of people learning to ask God for His guidance when reading the Bible. (This is one of the reasons that I am in favour of Alpha courses and the like, where people are actively encouraged to ask hard questions of God and the Bible)*

Why is this bothering me so much at the moment? I am not sure, I suppose I am readdressing a lot of things in my life. I am looking at what is most key and am aware that my faith is the most important thing to me. I feel closer to God now than I ever have. I am now at the point of understanding the idea of a constant companion, I now do not feel that I am alone. If I'm honest, I feel that I have opened my eyes for the first time and really seen the world in all it's glory. I now WANT to sing at the top of my voice during worship not because I think God will hear the loudest, but because I want Him to know how much I love Him and how thankful I am to Him. Bearing this in mind...I think I need to know that the thing that I am basing so much of my life on, is real to me...not that it says something because another person tells me it does, I want to be in charge of my relationship with God, strike that...I want God to be in charge of our relationship, not anyone else.

I have spent the last couple of weeks in limbo regarding my faith and my life and feel that I am coming out of the smoke, I am starting to see things clearer than I ever have, and I am excited and completely and utterly scared by it all.

*As a footnote...I am aware that the position that I am taking has it's flaws in that our own interpretation means that the Bible can be used for our own means and not God's. However, I am not proposing that we just read the Bible and think, what does that mean to me. I am asking that people give some air space to God in their reading and deliberation of the Bible and act on His advice. In the past I have prayed to God about something and really disliked the answer that I have been given but have had to follow it (albeit eventually in some cases!!) because God is a God that prods us when we need it.
Second footnote...The reason I do not like the 'God dictated it approach' is because my experience of it has been that people do not follow it properly, they interpret as much as the next one , only they try to make out that they don't. Everyone that reads a text, be it the Bible, or a novel, brings their own context to it, it is impossible not to. The problem comes when people do not realise this.*