With the MegaCab you shouldn't put anything under the rear seats as they fold flat to the floor. I went with a 10" sub in a properly sized sealed enclosure in the space behind the rear seat. I have seen similar arrangements with two boxes for two subs and one guy build a double sub box that pretty much stretched across the entire back end.
I used the hook section of some velcro (with a sticky tape backing) on the bottom of the box so it wouldn't slide around. The amp is sitting under the front seat.
All the RCA's, the gain control wiring and power wiring run along the door sills, past the kick panels (where the component speaker crossovers are) and up to either the head unit and dash or through the firewall to the battery.
Good luck with your mods!