It makes no difference whether the control surfaces in question are separate flaps, or is a set flaperons. The best way to check is to remove all elevator mixing. Set the model up for your normal approach speed and add the amount of down flap you wish to use. Compensate with normal elevator stick movement. You'll very quickly see which direction and how much compensation you need to keep your holding of the elevator to a minimum. Now set your transmitter accordingly. The amount may be much more or less than you thought, and it may not. You may be surprised.

It doesn't really matter wheter the model pitches up or down with flap deflection. You just have to find out which way it does, and then adjust for it. As a general rule of thumb, though, low-wing aircraft tend to pitch down with flap deployment, and high-wing aircraft tend to pitch up.

Work with the model up high so that you can play with varying amounts of flaps. See how the model flies at various speeds. Fly faster, fly slower, climb, descend, turn. Adding down deflection to ailerons may make your model stall more easily, and may even give you a nasty tip stall...it depends upon the exact planform, wing loading, and amount of flap. Find this out high enough so that you can take out the flaps and fly normally. Again, you may be greatly surprised...one way or another.

Enjoy finding out how your model handles with the flaperons. That's one of the more fun aspects of R/C flying...finding out how the model flies and then flying it to the limits and getting good while doing it.