Without knowing which card reader you have, and also not knowing what the reader's manual says about it....it's hard to answer.
UBB 2.0 internal mobo connectors have 4 pins, so it sounds like that's where it should go. Find out what the card reader's pins do, then check your board's USB header pin assignment (it's in the manual), and connect appropriately.
Low-cost asian-made devices are known for crappy manuals/info, so you may have to call them, and hope for english speaking tech.