When I shopped for a waterproof roof bag I went all over the place. I ended up finding the $15 job at Kmart to be the best deal for rooftop bag. It has all the straps and buckles you need to keep it well secured to the top of your truck without any cross-bars or anything like that.
I also got some tool drawer liner material in a roll to lay down on the roof below the roof bag to keep it from scratching the roof paint. It has worked perfectly for me. And, on a longer trip, or if I know I'm going to be going through a MONSTER storm, I might think about giving the zipper seams a layer of duct tape protection. But I've never had to do that and I've never had ANY leakage. However, as has already been mentioned, make sure you fold the zipper cover flaps down.
I have a bunch of waterproof bags, which I own because we kayak and canoe. It is possible to simply strap a number of these type bags to the roof, and they come in pretty big sizes. When I've done this in the past, I strap them down REALLY good, including a saftey rope through the D-ring. Personally, I'm a sucker for SeaLine bags because they have held up to some serious punishment for me. I did not buy the Thule bags because they are not certified for watersports. I won't stear you away from them because I love Thule quality on racks, but they are far from the experts on waterproof. SeaLine is a great manufacturer with decent prices. Check out Campmor.com for some clearance deals too.
