If you expect the circular holes to penetrate into the form, then you need to draw over an edge in the circle to form a face, and PushPull that into the form by the desired dim, to make a recessed cylindrical hole.
If you want a hole to punch completely through the form, then PushPull it more so it is completely through the form. Now select the new extended cylinder and use the Context-menu > Intersect with Model, to cut the cylinder at the lower surface. Now select the unwanted faces/edges of the cylinder and erase them. You should now have a hole that pass right through the form ?
