Not a lot you can do. Just leave the seats hinged up and allow to drain. If left flat like mine the water pools at the base and rotted the plywood base even though it was supposedly waterproof bonded ply. Made it go all soggy
The air holes in the base didn't really allow the water to drain away. They are really just to allow air to escape when you sit on the cushion to stop the vinyl bursting.
I also drilled in some plastic circular soffit vents in the back bench seat to allow circulation of air. That really helped as the box used to get really mouldy and quite unpleasant.