I completely forgot that the cab you have has a tiny little bench seat. I knew a guy who built something like a center consol and mounted a high quality 12 inch sub in it. It was a good idea because you did lose a little bit of floor space but you gained a small table/consol in the back...you just didn't set an open cup in it when the radio was going.
Wherever you mount the amp remember that they can get to be over 200˚ (I kept a thermometer on mine one time and watched it climb when the subs were getting hard use).
The wires will be fine under the carpet. I've got my CB antenna wire run down there and it is still good but you can go along the trim if you want to do it easy. I have found that the best tool to run wires is a decent length of weed eater line. It is stiff enough where it will push through stuff but is not so stiff that it can't make turns. When you get the line through just tape whatever wire your running to it and carefully pull it through.