[Spinnaker]

Put a rolled up bath towel in the fold of the window when you put the top down. This will make the window bend in a nice round curve, instead of a sharp fold. It will help prevent the dreaded cracked window at the fold. Since you don't have the sun to warm up the plastic, it is more prone to cracking because it is less flexable in the cold. I know it is a pain to get out and "throw in the towel" every time you put the top down, but is better than having to replace the window.
I store the towel in the space behind the roll bar and if you get one that matches the interior color, you can't even see it in there. The Sun doesn't come out very much here in Seattle also.
As far as caring for the plastic window, all I can say is, if you touch the window with anything, it will scratch it. The plastic is so soft, there is no way to you can do anything to it that won't leave some marks on it. The trick is to leave the least amount of damage and to repair and protect it afterwards. Never use paper towels to clean the plastic window and never use a circular motion when you do clean it.
Hear is what I do to clean and protect the rear window on my 2000 S.
I only clean the window when I wash the car. First, I hose off anything that will come off with the nozzle on the garden hose. Then I use a CLEAN sponge with soapy water to wipe any other debris off the window using a side to side "straight" line motion with gentle pressure on the sponge. Rinse it off with the hose and remove the excess water with a microfiber towel using the same straight line, side to side pattern. In fact, anytime you touch the window with anything, it should be with the same side to side, straight line motion, other wise it will leave swirl marks on the window.
I use the Porsche Polyglass Polish, with a soft cotton cloth, to remove any scratches in the window. Make sure you use the same straight line, side to side motion. The more accurately you are at maintaining the straight line motion, the better the window will look. I just started to use "Plexus Plastic Cleaner Protectant & Polish" to protect and restore the clearness to the plastic and I like it a lot. It does a good job of removing the last of the fine hazy lines from the surface. It is expensive, but you use such a small amount each time, I figure the can should last at least 10 - 15 years.
I have had a lot of people say that they didn't belive that the window of my car is ten years old. Most convertable top windows look like crap because the owners don't know how to maintain them properly. It is a lot of work, but it's the price you pay unless you have a newer car with the glass rear window.