JIPMER and AIIMS are not included in NEET,So you have to register and apply for it separately.After the exam is over and the results are out, you need to apply for AIQ, State Quota, Deemed universities, AFMC, ESIC etc separately as each has its own set of rules to follow. The counselling for AIQ seats, deemed universities ,AFMC and ESIC colleges is done by Medical Council online simultaneously. And the states conduct their own counselling for the 85% of state seats and the left over seats from AIQ.The left over seats from AIQ in govt institutions are transferred back to states while the deemed university seats are transferred back to the respective universities for filling up.Hopefully that would have of some help to you.