Your transmitter and receiver must have at least 5 channels to support flaperons. And the transmitter must have a flaperon setting to turn on. Typically, then, you plug one aileron into the normal aileron channel on the receiver and you plug tho other aileron servo into whatever the manual says (on JR transmitters it is AUX1 I think which is the sixth slot on the receiver).

If you only have a four channel system, you can still use an independent servo for each aileron. You use a "Y" connector to drive them both. And you put the servo arm on whatever side of the servo in order to make it go the right way. But you cannot implement flaperons with only four channels.