Actually I did.

In my quest in improving the sound quality in my truck. I removed all the factory gear including the factory sub and I kept the factory navigation radio, because I wanted to keep the factory look. The unit has performed really well with my after market gear with no engine noise
Your going to have two choices of mounting the amp in our trucks either on the floor board under the seats or where the factory subwoofer was originally installed. I chose the the location of the sub because it allowed plenty of airflow and I can access the amp if needed through the factory sub grill. The other option was to place it under one of the seats, but with adults and kids kicking it, I felt it wouldn't be a key location.
One amp you may want to consider is Alpine's 5 channel digital amp. At first I was worried of getting one, since I was using Zapco competition electronics in my other cars, but the alpine really gets the job done. Also with the 5 channel setup, it allowed me to install a sub base remote to control the amount of bass I was getting. Since I listen to variety of different music, I wanted to make sure I could control this.
I also applied Dynamat to all the doors including the rear door and that has made a noticible difference. The truck has made a radical difference on road noise not coming inside the truck. As for a sub I ended up making a custom sealed enclosure for a 10" sub. I wanted something rather small and deliver a nice bass note. It fits perfectly behind the 3rd row seat and is not obtrusive. Hope that helps you out and sorry for the long post