I charge per shipment/transaction. If you get 20 firearms in one shipment and pick them up in one transaction, it's one fee.
If you get 20 firearms from 20 different shippers and pick them up in one transaction, it'll cost you up to 20 times the basic transfer fee, but still only one background check fee ($10 to the state, here, to exercise your constitutional rights). I've charged a reduced fee in the past for several shipments received, but picked up at one time, provided it was for a good, repeat customer and they're not going crazy using me as their free gun storage unit.