There should be a scale option in your .FPE file. If not, check one of the .FPE files that came with FPSC; look for the scale line and change it accordingly.
If you want to make sure your models are scaled correctly in the game without having to alter the scale in the .FPE, a good way to do it is in the modeler program. Import a character, or entity that matches the size that you want your entity to be; then match the scale in your modeler, and save it to file.
-Keith
"Some people are only alive because it's illegal to kill them".