Hello dear, 

If you qualify jee mains then you can only apply for counselling of NIT colleges and for IIT you have to qualify jee advanced then you can apply counselling for IIT also. You can apply counselling for NIT and IIT  only through  JOSAA counselling .In counselling you have to choose  a list of colleges( with branch ) in which you want to be admitted in a  preference order then  josaa provides you the list of colleges you are getting according to your rank ,then you have to do payment to get that seat. 

Hope this helps you