In terms of Academics and Placements both are almost the same, Then comes fee where VIT has an advantage because fee at Manipal is Nearly double than that of VIT. From the campus Infrastructure point of view, Both campuses are equally good. But what makes Manipal better than VIT is its rules and flexibility give to the students, Unlike VIT here you will be free to do whatever You want.

So is shorts there are only two things on which they are a different one if fee and living expenses which are Higher for Manipal but it is flexible in terms of Rule than VIT so choose as per your Priorities.