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I've replaced the decks on a couple past Fords and yah, they have amps but are obviously relatively small compared to what you'll pick up aftermarket.
I have to say, the only think I don't like about my truck is the bass. I plan on installing a couple small subs under the back seat in the near future. I don't want to bounce out but I hate that when I have the windows down and turn the music up, the sound gets distorted quickly and the speakers cannot handle any amount of bass whatsoever. Sucks.
Obviously I have changed the factory headunit (not easily done on 09+) and thus have bypassed the factory small/underpowered amplifier. The doors are run off the head for now, and the moderate "thump" comes from the 8" JL. It's a crisp hard hitting little thing. I cannot comment on "how to" because I'm at a stage in my life where time is precious...so I pay the local shop to install. Plus, if it blows up, it's on them!
In my mustang, the OEM amp was in the truck, if I was to make an educated guess, I'd say it is going to be behind the dashboard - behind the a/c controls - that area.
A lot of it depends on whether or not you have the upgraded sound system.