According to the new IIT rules if you have less than 75%marks required during IIT counselling, and if you are appearing for improvement exams of 1 or more subjects then, the top 20 percentile cutoff will be considered.  If the board doesn't provide the 20 percentile cutoff, you have to get a certificate from the board stating that you fall in top 20 percentile.  

The other way is if you write all 5 subjects improvement exam,  best of two performance will be considered. 

So do it accordingly.