I was still working on this box in the photo...but here's what I used and I had no issues. Amp was mounted inside that compartment...for heavy rain, water, mud I prolly would have put some kind of breathable mesh over the open sides just to play it safe cuz I ended up in a torrential storm one night with the top up and windows out and my amp did have a lot of water splattering on it. Or mounting it upside down would probably help a lot too. Sub was a downfiring 10" and was a few inches off the floor. Box was coated with roll-on bedliner so it didn't soak up any water.
Keep in mind those of you that use carpeted boxes...if you get them wet enough they'll soak up water and fall apart. I highly recommend using bedliner as a coating.