Well I knew there were a knife projection, Though I use MS3D, is there any I could do about that?
I take a cylinder and extrude the side faces so that they fit the shape of a normal rectangle with a hexagon/octagon in the middle. You just extrude and flatten those faces so you essentially get a polygon hole cut into the rectangle. Rotate the shape to fit whatever your needs are.
If you haven't already, try out the positioning tool and selection editor. The selection editor lets you select faces in a 3D view, although it's half broken admittedly. The positioning tool lets you snap points, faces, and shapes on axes and lets you chose which direction to go.