Setting up the ailerons with a Y-harness is the easiest way to run two aileron servos with a radio. It can be done by using two channels on a radio (if the radio supports it), but in my opinion it's just a waste of a channel on the radio. The biggest reason why two channels would be used it to put flaperons on a plane, and those usually cause more problems than they are worth. Your best bet is to just set up the plane according to the instructions.

Ken