Yes there is a chance of getting CSE at manipal as manipal is given by too many students.From this,many of student take admission in different college.

You should start taking counseling of manual as early as possible may be little bit patience help you to get in main campus of manual

Otherwise you will easily able to get admission in different campus of manipal in cse

I think you can get other branches in it but getting cs could be slightly though so wait for counselling