If you have a base Laredo or Laredo E, then you don't have the fancy 9-speaker Alpine system. Thus no amp.
The wiring diagram available on wk2jeeps.com is for the 9-speaker Alpine system, not the base 6-speaker system we have.
The front woofers and tweeters are wire together. A cheap crossover on the woofer separates the frequencies. The front components and rear speakers are wired directly to the headunit.
The factory tweeter grills do indeed come out. I used them as the 1" Alpine tweeters I bought fit nicely behind the stock grills.
I installed the amp under the front passenger seat. There might be room under the spare tire plastic well, however you get no airflow there so an amp might overheat.
The only subwoofer I would buy is the JL Audio stealthbox that seamlessly fits into the right side of the cargo area. That's phase 3 of my overhaul. Probably do that later on this year.
I'm very happy with my new audio setup. It was a lot of work though. The WK2 is built like a tank and not easy to disassemble.