Personally, nothing I have ever seen as far as a boat cover is 100% water proof. I've had a few covers over the years. I spent as little as $125-150 for a generic one from Bass Pro or Overtons to the $400 custom tailored fit from the manufacturer. I will say the better the cover fit, the better the water runoff was and the better protected the boat was. I have a suspender system I use now that goes from bow, over the winshield, back to the stern. I also have a manufacturer custom fit cover from Nitro. Boat is always dry. When stored outside, motor is stored down to avoid buildup in the prop, and I jack the tongue as high as it can go. Water runs right off the back. Prior to getting this $400 cover, I had one of those $150 overton blue covers that was for a fish and ski 20-21ft. It fit ok. Water ran off ok, but still sometimes settled. So I bought some of that water proof camping silicon spray from the store and sprayed the entire cover. It helped a little bit. The cover was eventually destroyed due to towing and only lasted 3 years. So far, this newer cover is holding up much much better. Also, towing without the cover on seems to drastically extend the life of the cover. I had one cheapy silver one from Bass Pro and it didnt even last the summer even though it said towable right on the box. Right, it was towable, for about 20 miles on the freeway. It was cheap.
Now, you can also opt for a complete custom snap on cavas cover. My dad had one done that is practically waterproof it seems like. His cost upwards of $1,000 I think he told me and its the strongest cover I have ever seen. You can get them complete with snaps all the way round and pole systems, etc. His is even a mooring cover with thick velcro flaps to access the cleats etc. to tie up the boat. He trailers it long distances with the cover on (2years old now). And he also never has his boat shrink wrapped anymore. Cover survives two winters. I thought he was crazy, but he got what he paid for I think. I'll see if I can snap some pics of it this weekend.
The key is to have it tight and let there be no where that water can settle. So using poles as supports, using the windshield, suspenders like I have etc are some of the better methods.