That connector, referred to in the manual as ATX4P, provides extra power to the graphics card (PCI-Express x16) slots. Not all motherboards have this connector (or equivalent), but if it is present and you are using graphics card(s) then it must be connected, even if the card has its own auxiliary power connector (which must also be connected). This is usually due to the design of the board, specifically the current carrying capabilities of the printed tracks, and not the limitations of the main ATX connector. By having this extra connector, it is possible to spread the power load over more tracks than would otherwise be possible without it.