Generally, you can place two pins at the same point on your part and make one of them invisible.
Here's an example of how I do this with an ADP7182 power regulator:
Here, I have pin 6 and EP (the exposed pad) both mapped to VIN. They are placed over one another and the EP pin is grey in the Library Editor and invisible on the schematic. Notice that the pin names are the same ("VIN") as are the types and positions.