Considering both the universities are private, you need to consider different things while making this decision.
MIT is a renowned institution for all engineering, the mechanical branch has amazing faculty, good placements and best of the technology and equipment.
Also, UPES is famous for its chemical engineering related branches. CSE is surely not one of them.
Furthermore, you need to have a look at both places, how far are they from your hometown, and how easily you can travel there.
Manipal is hill station kind of place with beaches nearby. Also, this place is a university town, and therefore has very diversified life.
All in all, yes, Manipal should be your first option rather than UPES.
Also, if you’re inclined towards CSE and you’re getting mechanical in Manipal, there’s a good chance that in further rounds of counselling you might get CSE too.