Hi
Make a small box and set it up so its x,y,z coords are the same as the aleron,In the parts dialog call it l_flap or r_flap check the hierarchy node box.Then bring up the aleron part and in the part parent  select the l_flap or right flap.If you want to keyframe animate the flaps call the flap box lever_flap
Make sure you have flap enties in the aircraft.cfg
Cheers
Warwick