I don't quite see what you mean, but I don't think a basically square aperture should be all that much trouble. Perhaps what might have been better is to cut a basic square with the Knife tool, then, add and (re)position some vertices between the corners to describe any tricky angles or corners. Work with combined surfaces until you get the results you want, and then triangulate (if that's what your X-plane flight sim requires to render).
I had to use these kind of techniques to cut some intricate viewing portals in the belly of the Navy Buffalo. It would've been nice if the port was one homogenously subdivided square lattice shape, but, noooooooooooooooooooo......
Some windows were rounder, some were cut at angles, and the squares didn't all have the same dimensions....and the window went around the rounded belly contour of the fuselage: it took a lot of Knifing and surface combining to get what I wanted without creating a huge mess. But it worked out pretty good...
