Hi James, I was working on the same thing this weekend, sorry to be late on a comment. The one thing lacking on the instructions for the PD4045 is the jumper from the breaker slots to the "hot bar" (actually, it's one of the many things lacking in the instructions in my case). Don't feel bad about not understanding the instruction sheet, it's a POS as far as information is concerned and making sense. They build a quality product, but the instructions are for someone who has already done several installations, or perhaps works at the factory already.
In the image below, you can see the breaker area for my installation. Lousy about the picture quality, it's cropped out of a much larger image so the detail could be better & easier to see. The way mine is set up, breaker #1 (from the left) is the inlet breaker for shore power from the outside. #2 powers an outlet at the front of the cabin for the air conditioning circuit. #3 does the left hand counter outlet for the galley, the right-hand one is powered by an inverter off the battery. #4 is the jumper for the "hot bus" for the converter & charging setup inside the PD4045.

Another thing I'm confused about is the use of both red & black wires for the 12 volt power. What's up with that one, why? I couldn't figure out if the red wires were positive & the black ones were grounds when I started. I used my 12 volt "test battery" (it's next to the coffee cup & in front of the power switch) to check the circuits as I went, but it's maddening to have to do it this way. I still haven't powered it up yet, so not sure what will happen when I do. Hopefully everything will be OK when I plug it in the first time. As long as there's no smoke or fire, I'll be happy.