When I'm concerned about moisture getting into my pack I put my quilt in a dry bag. There are lots of brands of these. The Sea-to-Summit bag is one you hear about a lot. But you can also get decent dry bags at Wally World. They come in a pack of three.
If you had made your stuff sacks out of silnylon then you could improvise a roll-top closure and do just as well. With DWR you won't have the same level of protection. Cuben seems like overkill.
Check out Jim Wood's excellent article on keeping things dry in the pack. He explains how to do very well with a plastic bag and a "candy cane" style closure.
http://jwbasecamp.com/Articles/DryGear/index.html