HI Masheera.

Well yes you will have to for colleges such as AFMC and CMC, examination is the same but later you will have to fill their college admission form to be called for an interview. lest NEET admission form will suffice for many state colleges, you just gave to keep tracking the college of your interest for furthur details. Hope you do your exam well.

All the best

NEET marks would be considered wherever you go, 
so give neet with your best efforts,

and if you're giving JIPMER and AIIMS all the best for that too :)
For now, just focus on your NEET exam , you will have lots of time to fill up forms after that!
Best of luck for neet.