sounds like you got the same kit as me. The instruction manual is an older manual and the kit you have is updated.
You are right; the servos lay on their side on the ply plate and the control horn pokes through the slot... simply cut the supplied wire rod and clevis to attach to the aileron. To mount the servo to the ply plate, there should be some hardwood blocks in the plastic bags (with little slots at the bottom for the servo wire to pass through). i simply epoxied them on the ply and then mounted and screwed the servos to those.

What engine are you going to use?