This guy made a science out of it but it made my head hurt to read it:
http://microship.com/balance-your-boat-with-a-center-of-gravity-database/
Basically, from what I gathered after looking at the above site and others, your desired center of gravity line should be the appropriate angle from bow to stern on your craft that provides a stable platform at drift while allowing your boat to quickly plane, not porpoise, and behave well when cutting power from plane. If your boat pops up on plane, porpoises, understeers, and rears like a wild horse when coming off plane, yawing at the front and water nearing the height of your transom, too much weight is in the back. If your bow plows water, is slow to plane, wets you when running, oversteers, & dives when coming off plane, too much weight in the front.
I put my boat in the water to mark the water line before the motor was installed but frankly, it floated so high on the water their was nothing to mark. If the plugs had not been at the bottom of corrugations, I could have pulled them in calm water and it wouldn't have sank. Trying it again after the motor was mounted I noticed it appeared that more of my bow was out of the water than I expected but when my brother and a buddy climbed aboard it and moved from back to front I noted the spot when the rise in my bow submerged and that's where I put a large battery bank that was approximately the same weight as the two of them together. I put centered the 28 gal fuel tank directly behind them. It seems to have worked out well. When looking at the faint water line marks on the boat the margins between them seem pretty consistent.
Like others, I would suggest trial and error by temporarily rigging your boat with batteries and portable fuel tanks and using a couple of buddies as ballast to give you an idea how your boat behaves with the weight distributed in different ways.