i also faced the same issue when I got to know the result of Manipal entrance exam .i secured AIR 1119 in upes exam and was getting mechanical engineering
but then I decided to go with Manipal because of the following reasons
1-better recognition
2- better alumni network
3- better facilities
the only problem with Manipal Jaipur is that it has inexperienced faculty on the other hand upes Dehradun was established in 2003 . Plus upes is really good for core engineering and mostly core companies come for placement
hope this helps
best of luck