I have a slim 10" under my passenger seat (since i use the driver side with the seat flipped up alot) and then my amp is behind the seat. I think its a pretty clean set up
I got my box from supercrewsound.com and asked them to "flip it" since it was designed for the driver side. I lose my jack space but its too small with the lift and bigger tires anyway.

 

So amp was too big just placed it under the seat and put some bolts to secure it down, even my sub, sub box and headunit. If the thiefs want it, they gotta work their *** off to get it out