I would just do a proportional move like someone else suggested, but if you want a more complicated way: Build a model of the boat below the water line and try to balance it on a pencil. The model would need to accurately reflect the mass of the volume of the boat. For example you could make series of evenly spaced below-the-water cross-section out of cardboard, then glue them to a thin balsa wood "strongback" in their proper location. Then try to balance the model on a pencil or razorblade. The resulting balance point should be a close approximation of the center of buoyancy.

For this to work you need a fairly decent guess of where the waterline is then you need an accurate cross sectional shape at a series of points along the hull. Then you need to cut everything accurately and space it accurately... If you were creating a brand new design the effort might be worth it.