Having Sunbrella canvas means you really don't have to water-proof. The seams may need some attention occasionally, but in all the years we've owned our pop up we've never had leaks in the canvas or seams. The condensation on the bunk ceilings is an issue though. After a cool night and having several bodies inside breathing away it will happen. Keeping a window open or running a fan will help keep that to a mininum.
I see recommendations for the water-proofing spray that Bass Pro Shops carry as one of the best around. Since I've never used it don't take my word for it, but again I see it suggested often.
Now even with Sunbrella canvas remember the bunk end windows are canvas, and may need some attention. We've never had an issue with ours, never water proofed them.