ok, I think I know how to do this...To practice, first make a polygon plane with 1 subdivision along the width and height. Then make a polygon cylinder with o subdivision on the caps and place it above the plane. delete all of the faces on the cylinder except one of the ends. You should have 2 planes, 1 square, 1 circular, each with 1 face. combine the two objects.go to edit polygons>make hole tool and open the options. select second with the merge options and then using the tool, select the circle face and then the square face and hit enter.
Make hole tool only works with one face, so don't try to make a hole in an area that has more than one face. (I think - i may be wrong about that - have a play with the settings).