A good manufacturer of touring boats will probably have already addressed this issue, and you're in luck if you own or rent such a boat. The prudent mariner will check such matters before stowing gear in a strange boat. Open canoes, of course, don't face such space constrictions or ugly protrusions. Canoes with spray skirts and flotation, however, may have the same space restrictions and friction problems. If you're canoeing in an open boat, you probably aren't too worried about whether your dry bag will slide easily over other bags or grab the boat's sides.
Many canoeists use the roll-down top's buckle as a simple way of holding it to a thwart or seat.
This is okay in casual conditions, but your best bet is to install D-rings on your canoe's deck so bags can be lashed down with authority, particularly if you're carrying larger bags. Most touring kayaks have space for far more gear than a lot of us need, but stowing it should be done with the boat's trim and performance in mind. The same is true of canoes. Lighter items should go near the bow and stern, while any heavy items need to be along the keel line and near the boat's longitudinal center. The bow and stern should remain light and buoyant for good seaworthiness and crisp handling, and the boat's trim should be the same empty as laden.