If you make a seperate negative bus ... it should be pretty stout and located in the proximity of the engine. I'd recommend making the engine block itself your "negative bus" for simplicity ... it's the biggest chunk of metal you have anyways.
You could run:
1. a ground cable from the starter battery (-) to the engine block (rated to starting current)
2. a ground cable from the house battery (-) to shunt (rated to starting current)
3. a ground cable from the shunt to the engine block (rated to starting current)
4. a ground cable from the DC switchboard to the shunt (50A max house current)
Size the first three to carry starting current so that you can start the engine from either the starter battery _OR_ the house bank as necessary.
I recommend running the fourth cable to the shunt (instead of the engine block) simply because it would shorten the length of ground cabling for the house loads. Also, ensure you don't skimp too much on this cable size. You want this overdesigned since electronics (presumably you have some) prefer to operate as close to 12V as you can get them ... so minimize voltage drop here.
The echo charger negative can go anywhere on the negative bus, really, except for between the shunt and house bank.
As I describe, starting current will go from starter battery (+) -> starter -> engine block -> cable from engine block to starter battery (-) -> starter battery (-).
Right, on account of the alternator line.
It is a 500A shunt ... because it is. To be large enough to work for currents that large ... if, by chance, you were dealing with them.
1981 C&C 32