What kind of raft? Got pics? How big's the hole?
You can try patching it as normal, which is probably the easiest, but you may find that you're having trouble sealing the patch along that seam.
Depending on where exactly it sits and what kind of seams, you might be able to make a small cut away from the seam, patch inside, and out over the nail hole, and then patch the operating incision.
Personally, though, I would lean more toward using some urethane over the hole if it's small enough, and then sticking a patch on top of that.