Hello,
You need an aggregate of 75 percentage in CBSE Class 12th boards or you need to be in top 20 percentile of your respective boards in order to get admission in IITs. If you are appearing fir improvement, it doesn't matter how many subjects you appear for as it is completely upto you. You just need to pass all the subjects before appearing for improvement examination. As far as counseling for IIT is concerned, it won't cause any issue as long as you are having an aggregate of at least 75 percentage.
I hope this helps. For any further queries, ask me in the comments.