I was one of the first people to get the PA 200 amp alternator. Anyway I got rid of my stock wire and have just been using the #9909 4 gauge wire ever since. No problems. Didn't know you were supposed to piggy back them. Car has been that way for 3 1/2 years and 60k miles.
You can't run the stock wire with the 200A alternator, you would probably melt it. Look in the pic below for the difference in size. Considering the wire runs along the fuel rail a wire failure will likely cause an engine fire.
If you are running your battery to the trunk, I would use a 2 gauge wire if you can get it, you can buy it by the foot at a welding supply shop. You need the larger wire for the extra 10 feet you need to run, longer wires run hotter.