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My 00 had a sub box that took up half the trunk. My new 06 has a recessed space on the floor of the trunk that was perfect for a sub. I have a trunk again. I can actually put my gym bag, a medium sized cooler for soil and groundwater samples, a small cooler for cold water for me, and a foldup chair in the trunk. I'm in heaven!
with the others about using a cloth duffle that will fit down inside the well, then smaller ones that will fit on either side.
About the only thing that I have to add for general all around daily use is handy in my opinion. In order to keep the odds and ends from flying around inside the trunk, and to provide an unright spot for a bottle of Mobil 1, and a spray bottle of window cleaner up against the right side inner wall of the trunk. I took a clear plastic container that salad greens came in (Costco. It is about the size of the bottom of a shoe box) and attached two adhesive strips of the hooky part of Velcro to the bottom. While it is empty, one can put it in place and kind of wiggle it around lining up the inside edge with the edge of the well. This creates a space between it's outside edge and the inner wall of the trunk big enough for my Mobil 1 and window cleaner to be held in place. In the container, I keep stuff like my radar detector (that can not be used while I am in the Commonwealth of Virginia), a bungee cord incase I need to hold the trunk shut, Micro fibre towel, Z6, etc.
I did some research on the trunk rack. If you have a spoiler this is about the only one that will work. I didn't think it was worth the price. This is the email I recieved when I asked for info.
with the others about using a cloth duffle that will fit down inside the well, then smaller ones that will fit on either side. 
