It's swings and roundabouts really. The onboard headers don't have as much power as an addon board whereas the addon board takes up one of your expansion slots. It'll all depend on what you plan to plug into your ports. If it's mainly flash drives then go with a motherboard header, heavier things like iPods/iPhones/iPads, mobile phones external hard drives will be better served by an addon card.
USB 3 is backward compatible but itdoesn't work until your computer boots so plug your mouse and keyboard into one of the legacy usb ports.