Any wire connected to the positive terminal of any battery should have a fuse within a foot or so of the battery terminal. That means if you have a wire running from the front battery to a rear battery, there should be a fuse at each end of the wire. (If your two rear batteries are side by side, and you have a short wire running directly from one to the other, it doesn't need a fuse). The amplifier's power wire should also be fused near the battery terminal.
As a side note: unless you're planning to use the system often without the engine running, multiple batteries are almost always a bad idea. They can sometimes be useful in SPL competition vehicles, but for "daily driver" systems, they're likely to shorten the lifespan of your alternator.