It's been forever since I configured a transmitter with a wireless controller to work with RF and that was a really old version compared to what's available now. So only take this as a general direction and I probably can't recall a lot of it, so it's going to be pretty slim on that point.
First make a new model in your transmitter to be used. If you plan on several types... ie airplane, heli, multi-copter etc.... create one for each.
On my version of FS, it used a joystick controller driver... So you'll probably need to map the controls on the transmitter to the ones used on the controller in Windows. Once you do the general mapping... I believe you can then adjust the throws and other switches if there are enough controls enabled in Windows also.
Sorry I can't be more specific but the chances that the version of mine is anything like what you have are slim considering the number of years since mine was made. The manual will likely have more detailed info but remember that it is going to be generic since they can't cover all transmitters that are out there.
