No such thing as stupid questions!
1) Attach your power supply/BEC to the Wingstabi and power will then be supplied to the receiver via the link lead. Wingstabi will work on a 4/5 cell Nimh, 2 cell lipo or your BEC no problem
2) To program the WS via your PC you need the USB link cable and MPX launcher program (make sure launcher program is using the correct USB COM port, sometimes it finds it OK other times you have to tell it which port it is on). The WS must be powered the MPX USB lead does not supply power to the WS
3) You will need the receiver connected to the WS during programming and also the transmitter to calibrate the channels etc.
I assume that you are using the classic firmware and not the easy firmware. Note you will need to set channels on your Tx for Ailerons, Flaps, Spoiler, Elevator, Rudder, Throttle and gyro modes as a minimum, you can then also add separate channels for adjusting gyro gain if you wish etc.The Wingstabi 1.2.8 extended manual in the manuals section gives a good description of setting up a Heron glider with flaps and ailerons and that would be a useful starting point for a Funray.