For getting addmission in Amrita University your percentile should be around 95%. The university has started considering JEE Main this year. That too only 30% seats are to be filled through JEE Main. 

But your chances of getting into university also depends on branch you want to choose and your category.  

If you have given AEEE then definitely you can fetch a seat, as generally institutions cutoff through jee main are high and difficult and at the same time entrance through their exam is easy.