Well I'm thinking that if this alt. has a separate ground than the the case ground, you would still run it to the neg. post or frame. Unless you are trying to isolate a separate system totally? If so you will not be able to use the regulator for the truck if it's running the truck, you'd need a second regulator for the isolated system! You could possibly use a blocking diode between the stator wire on the GM alt. to prevent back charge or drain, but I'm not sure that will convert. You may be stuck to two systems. I'll work on this in my head for a few.
Can you give me a general idea of your intentions so I can put the system together in my head? Are you running a separate system or the whole truck also off this alt.?
Its done right or its not done !
Hail HHO.