I also have a 2000 Jetta. what do you mean by "I took one of the door panels off and saw that you have to pretty much get into the door to take those speakers out."? The tweeters come out pretty easy, and the main speaker is held in by rivets so you have to drill them out and when you buy speakers to replace them you need to get a mounting kit for them.
You could use the existing wiring if you'd like for the speakers depending on how much power you are going to be putting out of the amp. I would not use the existing power source for the amp though.
Keep in mind that a Monsoon amp really is not much of an amp. It is actually more of a crossover. Most of the amplification is done in the head unit then sent to the Monsoon "amp" and then the frequencies are divided to the tweeters and woofers. This means that you should have 4 wires going to each door. (2 + & - for tweeter, + & - for woofers)