You don't say what version of software you are using.
We are on the Dxd/Expedition flow and it is very easy to setup what you are asking, if I have understood correctly.
Within the cell editor we create our footprint with 16 pins, but number them 1-8 twice (so we have 2 x pin 1, 2 x pin 2 etc)
Then in the pdb mapping we have an 8 way schematic symbol which maps pin 1 to pin 1.
From the scheamtic point of view the symbol has only 8 pins, but from the footprint point of view there are 16 pins.
This is only one example.
We could have a connector symbol in the schematic with 1 pin, but the footprint has 20 pins (each one would be called pin 1) and everything maps fine.
Multi_pins_mapped.JPG 73.4 KB