I have stoneguard in most of the normal places they put it, including the on the rear cargo area.
However I also brought a Takla load liner that is water proof and covers all of the plastic area of the cargo area, right up the back seats, folds down to cover the load lip and covers the plastic bit on the rear door as well. That small piece is the only difficulty as when it is on as they sent it to me you cannot open the window part separately. They are looking into it and are going to send me a remade one, as their designer did not realise the door opened in 2 ways.
The only problem I have is getting the Velcro to stick to the new plastic, apart being fitted in very well and great padding; it sticks to plastic just under the cargo shelf with Velcro. New cars have trouble with being very slick and some coating protection I had put on when I brought the car stops the Velcro from sticking well. In time this will get sorted out.
The load liner is expensive $550 plus $40 to get the longer length is well worth it. Make the back of my Territory look like a nice padded cell. LOL
http://www.takla.com.au/products.htm for the range of products.
Mark