Covering a water-damaged rig will only make matters worse, because "out of sight, out of mind."
1. Fix the water damage. Don't worry, all trailers are garbage. Just use common sense, get your skill saw out, and cut out the rot. Then rebuild it. There is no instructions, because every trailer is different and equally crappy when it comes to water resilience. Use your best judgement on how to make the repair... I redid my floor with custom made floor joists that I laminated out of milled PT lumber. If you need to re do the roof, you've got a bigger job ahead, but again it's doable. The rubber membrane material will be your biggest expense.
2. Don't use a blue tarp, get a nice breathable fabric cover that will keep the rain and snow out, but let moisture (your enemy) escape.
Craig T. Bailey
2015 Jayflight 32BHDS
2007 Chevy 2500HD Crew 4x4 Z71