I've done a few long distance trips in a topless Jeep (just the bikini top, no soft top), and found that a couple of water resistant duffle bags like this:
Watershed Yukon Dry Duffle - Mountain Equipment Co-op
combined with a couple of back pack bag protectors:
Pacsafe Anti-Theft Bags & Travel Security Products
worked out great.
Everything stayed dry, and we didn't have to worry about someone just lifting the stuff out of the back of the Jeep when we stopped somewhere for food or gas or something.
Might be a bit pricey for a single trip, but I've had that setup for about 8 years now, and still get great use out of them.