When I cleaned out the trunk of my SE-R I used a Shop Vac, a hose, lots of Simple Green, and a big fat sponge.
I pulled all the carpeting and the spare to make my trunk basically a metal shell. Sprayed the sides and bottom with plenty of Simple Green and scrubbed. When I finished that, I hosed it down. There should also be a grommet under where the spare sits which you can pull out so the water drains. It was still a little dirty in the spare tire well so I washed it again with Simple Green.
At this point, Shop Vac the trunk out to get all the little pools of water (like in the little crevices to the left and right of the tail lights). The final step I took was to use paper towels and dry everything fully as well as remove any lingering dirt. I don't have any pictures, but this process made my trunk SPARKLE.
Getting water in your trunk under these conditions isn't a big deal. I had no problems with water getting anywhere it shouldn't. Just be careful with the hose and you should be fine. If you don't have a Shop Vac, just pull that grommet to drain the water and use a pile of paper towels/cloth towels to wipe up the rest.
