Whether you build the keel up of reduce the frame edges will first depend on whether or not all the frames are at the correct heights relative to each other. Look down the keel and see if any of the frames stick out vertically, or are out of vertical alignment compared to the others. If so, can you disassemble that outlying frame and rebuild it at the correct height? Just adding to the bottom or removing wood from the bottom surface edges of one frame will affect the top edge of the frame and the height of the top deck at that frame location. Hopefully you have plan drawing to refer to in order to check frame vertical positions.
I noted that at the bow, the keel protrudes pretty far beyond the frame edges, which doesn't seem right, from what know of those boats from a model of one Elco PT boat I built over 40 years ago.
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Take note of how sharp line is at the center of the keel. When you plank up to the keel, you will have to shape the wood to that profile. Right now, the frames in that area show in your photo above are suspiciously out of vertical alignment relative to the keel. You will have to add wood to the keel aft of the bow and remove wood from the keel at the bow to achieve proper hull contour. In the end, it looks like several adjustments will have to be made as you go in order for your model to have the right shape. Don't be afraid to make changes, as long as you have some decent drawings to work with to get everything where it should be.