George, the usual arrangement would be for the propeller shaft to emerge through the skeg at the stern. If you google something like 'small motor launch plans' you'll find a lot of examples.
The stern can be a very tricky area to plank as many of the planks have a lot of twist as well as complex curves and shapes. The advice above to construct a solid base for your second planking is very sound. It will also help if you carefully test fit the planks before fixing to ensure the shapes are correct. Don't try to force planks into shape or rely on fixings to make them keep their shape - make sure that they are the correct shape and have the correct curve and twist (if any) before finally fixing them.
Jim Lad's post in Ship’s boats with engines was marked as the answer