Which makes using FSDS2 easier.
FIRST - set your preferences to make a CFS2 model, and point FSDS2 to your CFS2 folder.
Open the file in FSDS2. - get rid of all the "previous version transforms, etc."
Rename your control surfaces, etc. as appropriate )r_aileron, l_aileron, l_flap, r_flap. etc.) For this, make sure you read the MS FS2K2 Aircraft Conatiner SDK. Note that the FSDS2 drop down parts properties box gives you the tags listed.
If you want to animate your wings to the flaps key, name your wings as l_flap, and r_flap *MAKING SURE YOU SET YOUR AXIS CORRECTLY!* note that since normal flaps rotate in the x direction, you'll have to move your axis to the right pivot point, and rotate the axis so that the x axis points "up".
Set you ailerons to be children of the "flaps" and hopefully you're on your way.
I have both fsds2 and gmax, but have not taken the time to do the tuts for them. Since the project is already in a .fsc format will probably try in fsds2. Any tips would be appreciated. Remember I am designing for CFS2