hi candidate,

I hope you are doing well. It does not matter what percentile have you scored in individual subjects. You will clear JEE Mains on the basis of your overall percentile not on the basis of individual subjects(PCM) percentile. You will get selected in the college on the basis of your overall JEE Mains percentile only. Getting 90+ percentile in 2 subjects cannot ensure you of clearing JEE Mains. If you score 90+ percentile in 2 subjects and performed very poorly(in negative) in 3rd subject. Then it will bring your overall percentile down.

I hope this answer will help.
All the best for the future!!