he motherboard SATA is better for high throughput, as it's quite likely tapped in to the high bandwith Northbridge/Southbridge chipset link, without draining PCI bandwidth.
Actually, most boards' SATA controllers are on the PCI bus. Only the very latest ones use chipset-based controllers. Many of them , if not all, are also RAID controllers so care should be taken in the setup process, especially when moving your boot drive to SATA. BIOS usually lets you set them to non-RAID mode. The biggest problem with MB SATA controllers is that most only have 2 ports. :sad: I stopped using mine because I needed 4 ports.