Leaked where the bunks meet the trailer? Like where the canvas attaches on top?
The pugs will not prevent leaks.
I'm not so sure spray repellent will help because the outside of the canvas is covered in vinyl. Try seam sealer around the patch and of course all the seams. When that's all dry have someone run a hose over the places you think it's leaking. You stay inside and watch. Once you determine where exactly water is coming in you'll have a better idea on what to do.
2013 Jayco Jayfeather X20 E, 2008 GMC Sierra 1500 Crew Cab Z71 SLE