should i prepare like firstly doing ncert portion of a paraticular topic then just after that doing iit portion or first clearing concepts of whole ncert then iit as whole

iam in 11 so i think ihave enough time

You are in class 11th. Yeah its true You have lots of time but believe me its not "enough" wat u just said for the preparation of en exm like JEE. DO NOT TAKE IT THAT EASILY..

2 years are too less to prepare for this exam..

Anyways as far as your question is concerned... Your first option seems to work the best way for now... The second option will work and should be applicable only when you are just about to give your JEE exam.. For now just ry to complete each and every topic completely.. Infact I wud suggest that you go through the NCERT topics real fast and spend most of your time on preparing for IIT related details of the same topics...

So best of luck for your preparations for JEE and keep writing...