About the Boolean first: you likely did not check the box that tells AC3D to delete the original object. So, when you do the operation you're left with the original, uncut house, and another copy of the house with the door cut out of it. But they're the identical dimensions, so you can't see it...and the original's covering the door!
As for your door extrusion problem, I'm not completely sure I understand what you're getting at... but I'll try and answer what I think the problem is.
If you create a separate door shape from a rectangle, and then extrude it through the walls, the wall will continue to show. But, if you describe the shape of the door in the wall with its own separate surface(s), and extrude these inward or outward, that should create the inside of the frame without any wall showing through.
Or perhaps what you need to do after the extraction is to go back and select any "wall" surfaces left behind and simply Delete them, creating a perfect hole.
If I'm not helping you, it's probably because I can't see what it is you're doing. If you can, post some screen grabs of your process.