If we're talking an Enermax split, then the main 20-ping/4pin connectors carry one 12v rail and power motherboard/CPU/onboard 12v devices.
There is one aux connector marked as 12v 1 or something, which uses the same rail as the main ATX connector plugged into the mobo.
All the other molex (4 pin) connectors carry the other 12v rail.
I have the main connector plugged into the mobo, and the aux for it plugged into my HS/F fan on the CPU.
Then the 2xHDD, 2xOptical and 9800 are connected to the other molex's, and use the power from the other rail.
Bearing in mind I used to use a system with ~15A total, and now have 13A + 14A, this should be OK, even if you have a few more drives (HDD's are ~2A each max pull from the 12v rail).
If you have a 6800 card, then I would put the main connector into the mobo (obviously), and the aux. for that 12v rail I would split into any HDD's.
Then the other rail (molex's) would be free for the graphics card, optical drives and any fans needing connections.