because I should take the microcontroller off the board (it's surface mount device)
If prototyping ALWAYS use a socketed controller. When overly optimistic, I have made boards that would hold two different packages of the controller.

connect it to some evaluation board or trying to "attach" an emulator to the control panel.

Connecting an evaluation board will get you nowhere, you may, probably will, be able to get a socket converter that will allow you to put a socket for the controller on your board and then you can use an ICE.

(I am a computer science student and I dont know much about electronics).

I do not know what your school will provide, but if your budget does not allow much, you may have to get by with a simulator (do a search on that word)

Erik