Mount the amp where ever you have room? I have mine mounted vertically on the wheelwell behind the rear seat. It's up and out of the way for the most part.
The only reason I wouldn't mount the speaker and amp on the floor is if you wheel where there is a chance of flooding. Not only up through the floor but through the doors as well.
I thought about mounting my amp under the front seat. Under the actual seat and not on the floor. Mounting it in a lockbox or on the back of the lockbox might also be an option too. Not much room under the dash, but if it's small enough, you could.
As for those Jeep boxes, I don't like them. They take up way too much room. You also get a crappy speaker and amp to go with it. That's why I prefer to DIY.
With my current setup, I can have the speaker out in seconds. THe amp just sits there but is off. That reminds me, I need to add that switch to the amp-trigger led. :roll: