Plug your card reader into the 3.5" bay. On the bottom part of your motherboard you will see a few input pins. Underneath of them if you look they are labeled. *Differs for different motherboard models*
USB1,USB2,USB3. the audio one is usally black and the farthest one to the back.
Okay now. The slot you are looking for is either of the USB ones. Which the pins look like this.
::::. or .:::: connect the cable from the card reader into one of these USB ports. *Warning do not force it in, if it does not go in easy. Check it is being pushed in the right way.