As stated above , one way is put the gear onto the body first, then install the wing. The downside is that the gear is in the way for painting and sanding.
Another way is to make the hole a little oversize, then install the gear and fill it in after the plane is covered and painted. If the extra clearance is in the form of a slot that parallels the thrust line (between the engine mounts), it won't really weaken the plane.