Hi there,
Do you have an image of the USB Pin assignment of the Card Reader you are wanting to use?
The ones on the motherboard are:
Row of 4 pins
1 - Power 5V
3 - USB DX-
5 - USB DX+
7 - GND
9 - No Pin
Row of 5 pins
2 - Power 5V
4 - USB DY-
6 - USB DY+
8 - GND
10 - NC
Although it might be OK to just connect the device in this manner it is worth making sure the pins in the card reader header are in the same order or you could have an issue.