I use car cards and waybills for freight car routing. Here is a simple method that requires no paperwork once it is set up.
There is one car card (the yellow card shown here) for each freight car. It is cut to baseball-card size so it will fit in a standard baseball card sleeve. The waybill is the white piece. It identifies where the car is going by a three-letter abbreviation, here GCF for Glen Cove Fuels. The train drops the car at Glen Cove Fuels, and the car card then rests in a channel on the front of the fascia. (The channel is vinyl molding made for bathroom tile).
After the operating session, the waybills are "turned" for the next routing. The waybill is just pulled out of the sleeve and tucked behind the car card. The car is now empty.
The destination for the empty is now revealed - in this case S for South Interchange. It will leave the layout via the South Interchange, and get removed and placed on the storage rack for future use.