Looking to install all new audio ('04 w/ JBL+Nav)

Well I'll start off with stating that I have no experience with any car electronics, but since I have purchased my first car, I'd like to put a nice audio system in. It started out with just wanting to replace the two front seat door sub-woofers due to them being blown, but since the car is in very good condition and only has 80k miles on it, I plan on having it for a long time.

So I was looking for some help as to what I would want to replace and what parts to get, I would go to an expert, but the closest thing I have to that is a friend with some experience, ABC Warehouse, and Best Buy. The latter two I considered, but I've heard so many negative things about those stores I'd rather do it myself with my friends help.

I know I'd like to replace all four door sub-woofers, but I'd also like to have a removable sub box in the back. I get the feeling that if I go that far, I am better off putting in an amp and new stereo too.

So in general I was just looking for some input from others who have successfully installed aftermarket sound systems in their Prius's.
What would you recommend? What should I avoid?

Any input is appreciated. Also if you missed it in the title; I have both JBL and a Nav in my car.