I am setting up flaperons on my 9C. The flaperon function works great for the ailerons, but I can't seem to operate the flaps. What am I doing wrong?

Nothing. The stock setup of the flaperons is so that the ailerons are operated normally, and then if you want to operate them also as flaps you will use airbrake or a mix to activate the flaps. If you want to be able to TRIM your flaps, or adjust them with a dial, go back into the Advanced menu, go to FLAP-TRM, make it active and set the desired % of flap travel on a knob. Note that the flaps will go both up and down on whatever knob is assigned to channel 6.