Well, the trick to keeping the quads is to make your cuts in a big loop, like so:

Then you go to either the plan or elevation view, and pull the appropriate vertices into position:

Keep making loops and and moving the vertices:

Change the view:

Repeat what you did for the other view. It gets a bit tricky here, because yanking the vertices at this stage will create some weird angles. Just go back and forth from this view to the perspective, just to make sure nothing wonky is happening.

And before you know it you'll have a spaceship!

About the quads not being planar:
You're absolutely right about that. Quads usually have a bend in them somewhere. That's where triangulation comes in. You can edit the crease without actually making a triangle:
