It looks like on the diagram they are showing some sort of breaker box. All I am adding is a second battery and a single audio amplifier. Will I simply connect the amp directly to that upper left post on the switch? (fused of course).

Also, and this is probably sad, but how do all of the other electronics in the boat wire to the battery? Right now on my single battery setup there is only a negative wire that goes directly to a ground and the positive that goes directly to the starter. When I add the second battery and switch will I need to re-wire the other electronics in the boat to go to the accessory post, or is it all smart enough to run the starting battery as a starting battery only and everything else will switch over to the house battery?

Thanks!

1) LEFT rear post so you will disregard the breaker panel and think of that as your resettable breaker for the AMP(s) then a long lead to the amps.
2) LEFT upper post goes to your existing fuse panel that feeds your switches and gauges.

"Accessories"

You should also have a smaller red wire with a large (most likely 50a) about a 8ga wire that runs to the dash fuse panel.

Would not use it. First off, you can not start your engine on ether battery alone. If the 1st battery is almost dead, the 2nd battery can discharge into the first one. By starting the engine on ether battery, this will tell you that the battery is in good shape. With this system, you will never know until its to late.

A dual battery set-up is cheaper and better. It gives you full control. Later you can add a battery combiner to charge both no matter how the switch is set.