Just a guess, but I would think the upper molex is linked to the upper slots and the lower one to the bottom slots.
With 3 580s I would connect both, I have always run with both connected just to be sure no problem here, from what I read if these additional supplies are not used, in some cases, depending on hardware, the mainboard 24pin connector terminal that supplies the pcie slots can be overloaded and worst case actually burn through excess heat.