It depends on your interest. If you are well aware of EIE and have an interest in the branch then choosing VIT will be better. However, if you want to play it safe then go for CSE//ECE in Amrita University.
I have a few friends from Amrita University, and according to them the rules are very strict and the curriculum is also a bit challenging. The exams of Amrita University are generally very tough and you will have to work very hard to clear all the exams.
According to the placement highlights of recent years, the average and highest CTC offered at VIT are 6 LPA and 39 LPA. While at Amrita the median CTC offered is 3.5 LPA.
I will advise you to do your own research on the branches and make a well-informed decision.