See if you want to go through the channels of JEE for IISER then also you will have to follow the same books as well as if you want to through the KVPY. So the books are the same for the entrance. After qualifying you will focusing more on science and other will be focusing on the engineering but else where there are no such differences.

I would say as you want to go for science you should have good understanding of the concepts as well as problem solving skills. This will intensify your research experiences further.

I hope this answer helps. All the very best for your future endeavors!