I was looking at some photos of your build log to get some better context of your build. I'm not that familiar with the HMS Onterio, but, if the gunports are meant to be perfectly flush with the hull, I agree with Bryian. If they are meant to portrude from the hull a bit, I'd take one of the planks that you'll use for the outer hull, place it next to the gunport on top of the rib/frame, and then mark that thickness on the gun ports. That way you'll have a better idea of how much the gunports will protude on the finished product.