I've got to patch the same holes in my car. You can get to it from the inside of the car.
Here are all of the helpful threads that I found in my searches when I was researching this for myself. I plan to fill the holes with caulking, smooth them down, and cover them with Dynamat type of Insulation.
http://dmctalk.org/showthread.php?16...ighlight=cubby
http://dmctalk.org/showthread.php?30...iberglass-body
http://dmctalk.org/showthread.php?11...quarter-panels