Hello Priyanshu,
IIIT, Bhagalpur and IIIT, Manipur both are governed by IIT Guwahati. However, IIIT, Bhagalpur is new and is in a developing area. IIIT, Manipur is relatively older and according to students' personal experiences it is better than Bhagalpur. Manipur's area is developed and all kinds of students study there.
Personally, I would recommend IIIT, Manipur.
Hope this information helps.
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