Ahh, you don't need flight modes for gear and flaps. I guess you could use them.. I usually just use mixes to do this sort of thing. Let's say gear is on channel 10. Just set channel 10 source to a switch you would like to activate the gear with. You may need to set up a custom curve to get the desired throw controls and or adjust the outputs for channel 10. But tht is the very basic way.
For flaps, you usually need to add a bit of elevator to keep the plane in trim, so whatever I am using for flap, I also add tot he elevator with a very small weight to add that elevator correction. Again, this is a very short explanation, what I actually do is a bit more complicated so I can adjust that elevator compensation in flight.
-Wayne