Why not just consider this the thread on different ways to create holes?

Here's another way in polys:

1. Place the cylinder (or whatever) over where you want the hole.
2. Open the Split Polygon Tool options and UNcheck Snap to Edge.
3. Draw a new edge where you want the hole to be.
4. Snap the vertives into place using the point snap (hold down V and MMB drag onto point). Remember to select which axis to snap and do it one at a time, unless you wan't it exactly on that point.
5. Remove the cylinder and delete the face, and you've got a hole...