molex pcie plug on motherboard

Solution
From your manual.
PCIE_12V (Power Connector)
This power connector can supply extra power to the PCI Express x16 slots on the motherboard. Connect the power supply cable to this connector when using two graphics cards. Failure to do so may lead to an unstable system.

So running one card you dont have to, two cards yes. My old Asus rampage 3 extreme had 2 molex connectors on the motherboard, the only time i plugged them in was when i was doing heavy overclocks on the GPU's. Was able to take a pair of 580's from stock core up to 998MHz with the extra molex plugged in. when i changed them over to a new board without the extra molex they could not come close to that speed.
From your manual.
PCIE_12V (Power Connector)
This power connector can supply extra power to the PCI Express x16 slots on the motherboard. Connect the power supply cable to this connector when using two graphics cards. Failure to do so may lead to an unstable system.

So running one card you dont have to, two cards yes. My old Asus rampage 3 extreme had 2 molex connectors on the motherboard, the only time i plugged them in was when i was doing heavy overclocks on the GPU's. Was able to take a pair of 580's from stock core up to 998MHz with the extra molex plugged in. when i changed them over to a new board without the extra molex they could not come close to that speed.
 
Solution
Thanks for the great answer, for some reason i could not find that in the manual. One other question will a hp oem psu 365w be enough to power a q9550 and a hd 5770. It has 300w on the 12v minus 20%=240w 12v, gpu max 110w, cpu max 95w= 205w plus fans, hdd and dvd drive=230 approximately. I also used a few power supply calculators and they all said that it would be good. But what is bugging me is that on the psu case it says it has two 12v rails one is 12A and the other is 14A. It says the 14A one is for the cpu and the 12A is for the rest. Are these actual rails or what.