Just so long as there are connections between everything, it doesn't matter where you ground what.
I have my battery grounded to the tranny. The tranny grounds to the frame via the crossmember, and to the engine block, via the bellhousing.
The body grounds via its contact with the frame.
All of my various electrical systems (horn, headlights, brake lights, coil) are grounded to something metal, and since all of the metal is connected somewhere along the line, I've got ground everywhere.
If there has been any modification done to your frame so that the engine or tranny doesn't make contact, then I would make sure that I had a wire running from the one to the other. In a stock situation, there won't be any reason to add ground wires except to ease your mind.
-Brendan
