From the Mophie site:
Which port is used for charging the powerstation mini and which port is used to charge my device?
Connect your cable using the bigger, rectangular USB port to charge your device. The smaller, micro USB port is used to recharge the powerstation mini.
Based on that, my guess would be that you use the cable that came with your iPhone (unplug it from the charger) and connect the USB end of the iPhone cable to the USB port on the Mophie.
If still in doubt, contact Mophie support:
http://www.mophie.com/support