The new ends you get will not be "canvas" anymore. Bear Creek would be using some sort of waterproof vinyl fabric - Sunbrella or similar. There is nothing that needs to be done with this fabric initially. Treatments can actually reduce the effectiveness of the waterproofing. That said, follow any directions provided by Bear Creek to maintain any warranty - don't take my word.
After a few years, you may notice that the water repellancy is starting to break down, and that is when you can start treating. My issues are usually around seams, and a good quality tent seam sealant will generally restore the functionality.
Otherwise just put the bunks away clean and dry; if you can't do them dry (rainy packup days) get them aired out and dried as soon as you can.
Congratulations on the new (to you) trailer. If you have pictures from the renovation, please post them! Once you have taken your trailer apart like that, you'll know it better than anyone and teach us all a few tricks I'm sure. I've done a partial floor replacement on my X19H that included removing most cabinetry. It was a fun and informative project.
ETA: Correction to above. Checking the Bear Creek site, they actually do use old-fashioned canvas. I would probably consider a different source that uses more modern materials. Canvas Replacements (canvasreplacements.com) uses more modern materials. Segment on the company from Rollin' On TV