Preferred Methods for making Apertures in Surfaces

Hello, I’ve been trying to create a space mining outpost hub - an enclosed building that connects to other buildings, which means I had to create holes in the mesh to allow those connections. So far, I made an interior wall by duplicating the exterior mesh and scaling it down, then created holes by using Subdivide and Loop Cut & Slide to allow me to have faces right where I wanted a hole (I then deleted the faces).

However, it’s gotten to the point where neither Subdivide or Loop Cut & Slide will work on certain faces. Here’s a picture of what I have so far: http://i82.photobucket.com/albums/j252/Tohron/BlenderOutpostPic.png
(the diagonal faces are the ones where the subdivision tools don’t work at all)

So basically, I was wondering if other people had more effective ways of inserting apertures into a surface - for doors, windows, or whatever. Thanks!

For more difficult hole like you have, try it out with Boolean modifier first. It may not give you what you want, but you can see how Blender solved the problem. Then, clean them up.