The wisedom I've heard on applying fiberglass patches is to put the smaller pieces on the surface of the larger pieces. This prevents sanding through too many strength-giving long glass strands as you fair in the edges of the repair.

If you've already sanded away a significant amount of wood you can still patch on the inside of the hull, as long as the deck is not in place.

As an aside, I don't thing the deck will make any difference to the shape of the hull on a Chesapeake.

You might try calling CLC for their advise on the matter; they've probably heard of other people who have encountered the same problem you've got.