You don't have to fill individual applications for NITs and almost all CFITs. They are all covered under THE JEE Mains counselling, for which the portal opens up after results.
IIIT Hyd for example, it's application has to be made separately through its Web site.

Hey,
If you are not interested in jee advance then yes you can start filling colleges which refer to jee mains marks. But still you can fill when you get your rank, so seat allotment will start in June end or starting of July.
All the best

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