I would make sure you have the flap switch assigned to the right channel. I use the V-E switch for it here, so I can get them with my finger without taking thumbs off of the sticks. Go into the Aux-CH program on the 2nd page of the basic menu, and make sure that you have channel 6 assigned to whatever switch you want to use there. That should make the flaps work regardless of the flaperon setting.

Then one of the P-Mixes in the advanced menu can be used to trim the elevator when you use the flaps. You will just have to make sure the right channel number is entered in the mix. (sometimes it will say flap for say chan 5, but youre really using it on 6, have to make sure) However, I would fly it first before setting up the mix, as some planes dont need it.

Hope that helps....