So lets say I have the potential to draw 700amps with my system,

If I have 1 battery under the hood and 3 more in the trunk,

a run of 3/0AWG wire front to back, how do I fuse it?

Last time I checked the largest ANL fuse was 300AMP

How do you guys with monster systems do it? other than multiple runs of power wire.

With 3 batteries in the trunk, I seriously doubt you will ever pull enough current to pop a fuse that big. Unless you are trying to draw way to much power for those three batteries, they act sort of like an electrical shock absorber and supply the spikes that your system needs, while the wire from the front will keep current flowing from the alternator to keep the rear batteries charged. As long as the fuse or breaker isn't too much for the wire (not a problem in your case with 3/0!) you are safe.

I like the idea of a circuit breaker (the largest I remember seeing for car audio is a 200 amp I think) so you can just trip it if you need to cut the power for any reason, then reset it again repeatedly.

Also, a large inline relay, wired to separate your front batteries from your rear bank when the key is off, will prevent the two battery banks from draining one another. This will also allow you to run the stereo some with the car off with no worries about not being able to start the car if you run the rear bank too low.

I'm no electrical engineer, but that's my take on you situation. I'm interested to hear from others.