Connecting your 12 Volt return (not actually a ground) to the hull is something you are stuck with because the engine block is the return for all the engine circuits, and the block is connected to the hull. Most Marinettes seem to have a stud in the hull in front of and between the engines. Battery negatives go to the stud, and a heavy wire runs over to the block.
This is fine, but the preferred way is to run heavy wire from the starter directly back to the battery, eliminating the connection at the stud. In any event, the battery negative ends up connected to the hull.
You probably don't want to let the secondary of the isolation transformer (tranny?) just float. If the hot side shorts to ground (hull) then the neutral side will become hot and the breaker will not trip, both bad things. Most sources say to connect both the neutral (white) and ground (green) to the hull for proper breaker operation. This connects the metal frames of microwaves and stuff to hull for you via the green wire, and keeps the white wire near ground potential where it belongs.
Be sure that the dock power goes only to the primary side, with the green connected to the shield or frame. Be sure the dock power green is not connected to the hull. The whole reason to have an isolation transformer is so you don't have to have the dock power green connected to the hull.
Don't be concerned that the hull is being used for both dc and ac grounds. Just be sure that the connections are made at one spot only. For dc, that is probably the stud in front of the engines. For ac, it is the isolation transformer secondary white. The green to the outlets also goes to the hull.
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida