I know what you're going through so I will do my best to answer your question. If I understood you clearly, you want to know where do you draw the line between your head/heart when it comes to following God. (Correct me if I'm wrong).
Let me show you how it works for me. My relationship with God is like a Father-child relationship. I believe that is the liberty God has given me - to behave as how a child would behave with his father. I am allowed to play within certain boundaries. These boundaries are defined by God's love for me and by His chastisements.
I am not a person who would accept anything merely on face-value. I need to be fully convinced about the matter before I accept it. I follow the same principle when it comes to believing in God and in His Word. I believe that this is the liberty given to me by God (I thank Him for it), albeit with certain clearly defined boundaries. I can question, prove or debate with Him as long as I don't cross these lines -
- God is beyond my intelligence and is far beyond my understanding.
- I may not understand or know everything owing to my limited intelligence.
- God always has my best interests in His mind - even if it is a situation/issue I cannot accept right now.
- Being the Redeemer of my soul who is more concerned about my soul in eternity, He has the liberty to lead me through paths that are contrary to what I have prayed for.
It is like how a child may not understand his father at all times. We can try and reason it with our limited intelligence but there are certain questions to which we may never receive the answer. The only answer we can give lies in Romans 8:28.
Let me share with you one personal experience which rattled me. A couple that I was close to were going through a very difficult path. The husband was diagnosed with brain tumour which was in an advanced stage. The couple had only been married for two years and they had a baby girl who was about 8 months at the time when he was diagnosed. To me, this felt like a test of faith for the couple - where God was trying them to see if they still loved Him.
Though his condition worsened and he had to go in for chemotherapy, we all believed that God would lead them out of this victoriously. So firm was our faith that I think most of us (those who were close to the couple) were praising God in faith for the healing He was to give the husband. And he did start recovering well. Though the tumour left him paralysed and he lost the ability to speak, he slowly started regaining them. Within a couple of months, he was able to mouth out a few phrases and lift his fingers with some difficulty. I was so sure that God would soon raise him up and make him a testimony. But all of a sudden, his condition deteriorated. He stopped responding to treatments and it looked like a relapse. Unfortunately, after suffering for a couple of weeks he passed away. This was a big blow to all of us. I found it hard to accept that God had done this to a couple which was so happy in Him. I refused to accept it and I questioned God over and over again about this. It is only now, more than a year after his demise, that I have accepted his death and that God has the right to do things with us as He pleases.
What I want to tell you is that we may not always understand what He does. Yes, we can question God about it and try our best to understand why He did what He did. And God, on His part, will answer our questions. But if we don't get the answer for our questions, then we must realise that He is beyond our understanding. Our God is an awesome God.