post up some pictures of what youre explaining....it will help us figure out if its right or wrong.
From what I have read about bungs.....you want to keep them a couple inches long out the back. This will help your boat from sagging in the rear over time.
Also, if youre seeing a gap between the boat and the bungs in the intake area, you might have a bad hook. Put a straight edge on the bottom of your boat to make sure its flat from front to back. A bad hook will cause some major handling issues on most boats.