So I've had a system built around an Asus Maximus III Gene motherboard for the past few months. The whole system has really met/exceeded my expectations and good lord is it stable/fast. However, as I was assembling it I recall having a question and instead of doing the proper thing and asking the community, I just went full speed ahead. Obviously I haven't damaged anything, but my curiosity has gotten the better of me so I thought I'd bring it up.
My motherboard had two 4-pin connectors in addition to the standard ATX power connector. My PSU (Corsair 650 HX) had two of these connectors that matched up so logically you plug them both in. Well, one of the 4 pin connectors (on the motherboard) had a plastic cap sealing it off... it was firmly fitted into the 4 pin connector as to prevent anything from being plugged in. I just forcefully removed it, plugged everything in (I know... not the smartest move) and prayed for the best. The system is rock solid stable and I haven't really thought about this much since I built the system in early October. The motherboard's manual was worthless and didn't really clear up anything on this topic and a visit to the Asus forums didn't yield any positive results. I guess I'm just curious... does anyone know why Asus would cap that 2nd 4-pin connector? Is there any chance of long-term damage to the system board if I leave it as-is.
You mentioned the PSU comes with 2 x 4 pin 12v. auxillary power connectors. No matter if one or both are plugged in, the power supplied from those connectore is still .12v (total). Uisng both 4 pin 12. aux. connectors would provide a better ground, but would not supply any more power than 12v. (total). I suspect the MB was capped so not to confuse should the PSU has only a single 4 pin auxillary lead.
You were correct in plugging in both 4 pin 12v. auxillary leads to supply power to the CPU. Especially a quad or OC'ed quad that can use the extra ground of two 12v. power source draw point. Video cards with multiple 12v. power lead requirements do so by the same principle. Not to supply 'more' than 12v. power, but a better grounded 12v. source.
Also, besides the 24 pin main power lead from the power suppy, every lead from the PSU provides 12v. current. The other voltages requirements are supplied by the MB through voltage regulation.