The difference between Applied Computer Science and Software Engineering is big. First of all ACS is in Enschede and SE is in Deventer. The subject matter is also different, with ACS the focus is on embedded systems. SE has three specialisations: programming, business it, server management. If you don't want to do embedded sytems SE is the right choice. Depending on how much work experience you have, both studies might not be very interesting in the first year, but for most people the second year is a lot more interesting.
Hope this helps,