The controller can be any place. Integrated into the chipset, an add-on chip built into the motherbd (try to find out whats its connected to, usually a pcie x1 link), or an addon card like you're looking into.
Ok lets say you put a WD Raptor drive in an external usb3 enclosure and lets say it can transfer data at 150mb/s just for the sake of the example.
if you plug it into the usb2 ports you would see something in the mid 30's to 70mb/s depending on the usb2 controller your plugged in to (some can do 2x speed)
if you plug it into a usb3 pci controller you will see about 128mb/s (133 minus headroom) but anything else on the pci bus needing bandwidth would subtract from that figure. The PCI bus 133mb/s is total bandwidth, not per...