It really depends what kind of a hole you want. My advice would be to create a circular formation on two faces that oppose each other then simply use the bridge command (=)
to create the circles or whatever you want the hole to be I would first inset the faces you want, then tweak the vertices you want (if you want a perfect circle I'd advise using an n-gon as a quick reference when dragging vertices.) Then to make sure the face is flat, I would select the faces and go, "Edit>Flatten..." and choose "Normal" (that step is only if you want the face that you inset to be on the same plane as the original face.) You can then select the two inset faces and press "=" which is the bridge command.
