It's fairly easy to do this:

Step one:  It can be done only in the vextex room

                      Make your main cube and make your doorway cube, move the doorway cube inside the main cube so that part of it is still sticking out.   Then hold down on the left mouse button and draw to enclose both the main  cube and the doorway cube.  Press down on both the ctrl and alt keyboard tabs at the same time and select a point on the main cube  AWAY from the merger.  That point  should change color.  Then go to your boolean drop down menu and select boolean substract operation.  The hole is formed inside the main cube.  Jan