Is it possible to only fill a Li-ion BMS partially?
Is it possible to use the BMS with only, say, 2 or 3 of the 36v packs
  of cells I made? The use case would be for a lower capacity pack...
  
  If so, would I have to wire it in a particular way? Such as connecting
  the charge/discharge positive to B2-B3 instead of B10?


You seem to be confused about capacity and number of cells. Connecting to B2-B3 would lower the voltage, not the capacity. It also probably wouldn't work with that BMS (Ali-express locks up my browser so I can't check its specs).

If you have several 36V packs then you can wire them in parallel for higher capacity, but each one should have its own BMS. If you make the packs yourself then make sure the cells are all identical (same part number, same voltage within 0.03V, same age - preferably new) or the BMS may not be able to balance them (assuming it even has a balancer).