you'll also be happy to learn that when you take an open edge, holding shift and draging it will create a new polygon.
for your spaceship aplication, you obviously have a curved shell opened on some locations, with more blocky structures inside.
i would do this shell first, having my holes whereever i want then only making the blocky structure.
(and for the curvy shell holes, delete your polygons instead of extruding them. you'll be wanted to apply a shell modifier on that later
)