For cleaning mold or mildew stains, do NOT use bleach or bleach-based products. This will hasten the deterioration of the canvas as hand-washing and rinsing canvas in place will not be able to remove all of the bleach.
Use something designed to remove mildew on canvas such as
Iosso Mold and Mildew Stain Remover.
It is non-toxic and specifically designed for woven materials. It works well on vinyl, too. I have used it and am glad that it really has no odor which means you can use it in enclosed spaces, such as inside your PUP. Just cover everything with plastic and towels where it might run down then clean it with this. It is also biodegradable so whatever does rinse away won't be a problem.
Bathroom cleaners that use bleach and other products are designed for use on non-porous surfaces like tubs and counter-tops. Canvas is porous and mold spores are smaller than where these cleaners will penetrate to. Sometime down the road, you will likely get mold again at the slightest provocation of moisture as you never removed all of the mold with the bathroom cleaners. Often, you become paranoid enough to keep the canvas dry, or dried out afterwards, but one slip up and mold can grow back faster than ever. Plus, with the deterioration of the canvas sped up by latent bleach still in it, you're looking at replacement canvas sooner rather than later.
Long story to say please use the right product. I did have to use a little elbow grease but knowing I wasn't harming anything was well worth it. $1000 for new canvas is a steep price to pay for learning that one the hard way. No thanks.
As for waterproofing the canvas, if it is indeed canvas, is outside of my personal experience. I have vinyl and Sunbrella (which is a synthetic canvas of sorts) for my tenting materials. I do know that
303 High Tech Fabric Guard will add water repellency to most any woven fabric. It is safe to use on canvas. I know some other canvas owners have mentioned what they used but can't recall at the moment what it was.
I do know that you should
NOT use the silicone sprays found in most camping sections of most big box stores. It is very short term, does not really penetrate the fabric and attracts dirt which worsens the problem of water repellency in the long run.