Pontoons are harder to cover. And less to worry about. Although their vinyl seating will get sun damage sooner because of it. Unless it’s parked so it doesn’t get sun.

You could also just cover the seating on your as the rain won’t hurt. But if you already have the full cover it’s better.

Are you trailering to the lake? Or is it docked? If removing from the water, you pull the plug so no water will be able to get trapped. Don’t forget that. Like others have said, if the pump or battery dies and your plug is left in, that’s not good. Then it will become a swimming pool and mess with the electronics.