I would cut out for the retracts before sheeting it. The mounts for the landing gear brackets have to be spread out through the foam for strength. in fact, the fore and aft ones should go all the way to the leading edge and braced to the leading edge spar. The wheel wells should be also lined to the foam surface to glue to the sheeting when it's installed.
Don't forget, those once in a while rough landings have to be taken up with those gear mounts.

Gord.