Water gets everywhere at some point, so raising your enclosure off the deck with ABS, HDPE or Starboard polymer blocks is mandatory. They'll serve as both risers and mounting feet.
If your box is resin coated it will shed water effectively. However, resin is micro-porous and will wick water up from the deck. Elevating the box eliminates a moisture trap.
Polyester resin will get the job done. Epoxy resin is better and bed liner, if applied thick, is pretty much waterproof.
You can cover your resin-coated box or facade with marine-grade carpet. It matches your interior better, won't mildew or fray like trunk liner, plus the rubber backing provides a water barrier.