My car cards aren't too unusual, except in their size. I prefer cards larger than the Old Line Graphics style, yet I don't want them to become unwieldy. So I wrote some software to generate the cards I wanted. They're 2.5" tall x 4" wide, with a pocket on the right side.
(The Gimp source for this carcard is available.)
The waybills that I have today are hand-written. I haven't yet gotten around to writing the code for printing waybills, mostly because I don't yet have the full list of industries. I'll need that, plus the final sizes of my staging yards, before I'm convinced that my billed destination mix isn't unbalanced.
I use a system that handles variations in how long it takes to load or unload a car (example: unloading a tank car full of gasoline is a matter of a couple of hours; unloading a boxcar full of 2x4s will take several days). So each waybill is noted with "1 day to unload" or "2 days to load". As each car is spotted, the carcard is to be placed in the appropriate box (there's a box for each day from 1 to 3). During restaging, the cars in "day 1" are moved to "pickup", and "day 2" is moved to "day 1" (and so on down the line).
Waybills are rotated when they move into "pickup"; and the bill is removed from the car card at the end of its cycle. This car becomes an unbilled empty, and is routed according to the instructions printed on the car card. It is also eligible for re-billing, as I will pull a new set of bills for each session. Those bills are to be distributed around the layout to any suitable car.
Certain bills have instructions that must be met when being placed initially. An example might be a bill for auto parts from Ohio to the Ford plant. I don't want this bill magically appearing in the yard (from an no bill car), nor do I want this car coming in on the NP transfer. These bills are marked to arrive on a westbound transfer run, with certain preferences (most of these cars came in via the Omaha or the Milwaukee).
Any car that reaches staging without a bill, and remains without a bill at the end of the restaging process will be removed from the layout until it is needed. This keeps the car fleet in a rotation, so we don't see the exact same cars in every session.
Confession: this doesn't happen yet, since I don't have enough cars. But I plan to do this, as the car fleet expands sufficiently.