A trick I've used in the past is to cut several pieces of wood tongue depressors and glue them to the inside surface of the hole so they overlap the repair piece. Clamp them in place with clothes pins or something similar. Once they cure, they'll provide a shelf for the cut-out repair piece to sit on so your exterior is perfectly flush.

Be sure to mark a line with a stabilo or wax pencil so you can align the cut-out properly back in the hole (particularly if you are cutting a round hole). This way if there is any discrepancy in the thickness of the skin or core, it won't cause you issues later during fairing.