It's nothing fancy, but I use a heavy cloth tarp over the back cargo area that folds up the sides a few inches. I fold under the excess width and length of the tarp to fit the space. When the back seats are folded down or completely out of the vehicle I unfold the tarp to cover the whole area.
When I go scuba diving, especially beach diving, I use a waterproof tarp that can cover the whole floor.
Check out CanvasBack.com They have the liner for the floor, but they also have the pieces that fit over the wheel wells. I have the entire set and LOVE them...
I can send you a picture if you are interested...
Although I don't own a set of these, I've seen them on other rigs and they are pretty nice. The wheel wheel covers and hatch gate cover that are optional with these are pretty nice too from what I've seen.