There exist a number of different interfaces, which can work with FMS. Most of them (simple "Windows 9x-only" serial and parallel, serial FMS-PIC, USB FMS-PIC) are proprietary to FMS and, by no means, can work with RealFlight.

The only other interface type I know, which can work with both FMS and RealFlight (as well as with many other sims), is joystick interface, either game port or USB. Such an interface converts PPM signal of your transmitter into the virtual joystick, which can be used by any Windows appication supporting joystick input.

If you have this type of FMS interface and your only problem is to properly configure RealFlight, you may want to look at the help pages here:
http://www.milehighwings.com/manual.htm

Hope this helps,
Boris