I think it is better to keep the batteries maintained. If you don't want to leave them in the boat, then make sure you store them on top of wood blocks and not flat on concrete or the ground.
Brace the cover from underneath, snow accumulation will sag the cover and you'll end up with leaks or a rotten cover. I would also buy some cheap screen door mesh, block off the openings under the cover at the back of the boat. wild cats, skunks, racoons all love a cozy covered boat during the winter. Learned that one the smelly way. You need to have ventiation under the cover though, hence the mesh.
Most of all, just be sure to apologize to the boat on a weekly basis. Tell her you still love her and this is only temporary.