With hundreds of cables involved in connecting your components, you'll need to be careful and logical in placing each audio or video unit on shelves or racks. You also should take care to label and group cables and components.
When it comes to setting up your home theater, you'll find that you'll spend as many hours connecting cables and wires as you spend tweaking the picture and adjusting the sound. And, as you'll always find some new piece of killer gear later on, this isn't a one-time operation; you'll be back in that morass of cables again and again. Taking some time to figure out where best to place your components will save you frustration, hassle, and wasted dollars on additional, longer cables down the line. From there, you can use labels, a bit of Velcro, and banana plugs to take the mess that is your theater setup and turn it into an organized, easily maintained audio/video system.
As a general rule of thumb, put your amplifier on your very lowest shelf. It's an incredibly heavy unit, and you don't need it breaking through and crashing on top of another unit. Place your audio processor or receiver on a shelf just above the amplifier, for the same reason. Additionally, you'll have a lot of connections between your processor and amplifier, and this will allow for shorter cables to be used. If you have a receiver instead of an amplifier/processor combination, just place it on the lowest shelf you've got.
Moving upward, ...