As someone who tows their boat 300+ miles almost every other weekend, I only will tow with a cover. The boat pulls sooo much easier, don't have to worry about an errant rock taking out my windshield ( I've seen it) and I don't have to stow everything to the point of making it hurricane proof.
That said, in my opinion, the ONLY way to trailer with a cover is to have a custom cover made that snaps to the boat, no straps going to the trailer or anywhere. Adjustable poles are used to hold the cover up and tension the cover. If the cover stretches, the poles can be adjusted to take up the new slack in the cover.
I've had 3 custom covers made (3 different boats), all from a fabric called Top Gun, or now Top Notch, it's Marlen Textiles product. Over the literally 1000s of miles towed with each boat, never once did I have failure. Maybe a couple times a snap came loose but that was easily fixed. The latest cover for my 20' Lund came in at about $1100.00.

