How do I deal with keg and crate deposits or credits?

Create a stock item like "Keg Deposit" (naming the specific product), assign it under a Beverage category with a default supplier, and add it to purchase orders when new kegs arrive. When the deposit is credited back, raise a credit request for it and receive the credit at the value on the supplier's note. Stocktaking deposits is also worth doing, so you can confirm suppliers are crediting you correctly.