Dear Leena, AIIMS and JIPMER are autonomous Medical colleges which conduct their own medical entrance examinations to fill in the seats in their respective Medical colleges. NEET has got nothing to do with them. Usually each college has its own way. Few medical colleges release their online applications well before NEET and you need to register and fill in the application. Few colleges wait until NEET results have been declared and declare their cut off for various categories and then allow only qualified candidates to apply online. So it depends on the Medical college that you are interested in.