Ah, you are referring to the section which states "To Engine Negative or Bus".
I doubt you have a "Negative Bus Bar" installed on your boat. There is technically a negative bus bar attached on the 12VDC fuse block(s) under the dash, but I wouldn't bother running the charger all the way up there.
You could technically consider the entire common ground system as a giant 'negative bus'. You should be able to tie that into the common ground almost anywhere.
The wiring diagram shows all Positive connections to all Batteries. If all of the batteries negatives are wired together (which I assume they are) then tie this into any negative on any of the batteries.