We charge a $50 deposit on beer kegs that are sent out, along with the cost of the beer inside. I'm working around the issues below, but a few (hopefully simple) changes would make things a lot easier for us.
1) We are charging deposits as services on the item invoice, since there is no physical inventory to track. However, there is no quantity field in the service area (which DOES appear on the service-only invoice), so it isn't obvious to me or our customers if that number is correct. The simplest solution is to add a quantity field, so that I can type in (and see on the printout) that 35 @ $50 = $1750.
2) The deposit "sale" is not an income item, it's really a liability which we will have to pay back out at some point. However, you can only choose an income account when creating/invoicing the service in Dear. I've hacked it by creating the item in Dear, syncing to quickbooks, changing the account to the appropriate liability in QB, and then syncing back to Dear. The invoice then shows and charges against the correct account number, even though it isn't normally available in the dropdown.
Even if it requires a second click (like "Show all accounts" in the dropdown), it should be possible to sell against a liability account for deposits.
3) Finally, we issue a credit note to our distributors for the deposit when kegs are returned to the brewery. Keg returns are completely unrelated to shipments, so it doesn't make any sense in our setting for the credits to apply to a single sale. (Though that would make perfect sense when selling a serial-numbered product, or when your customer only had one or two past purchases.)
The workaround listed on the support site is to create a sale, discount it by 100%, and then issue a credit with 0% discount. That's what we have to do for now, but it's many more clicks than simply having a "New Credit Memo" link on the Sale menu, and it wouldn't work when you are crediting an inventory return, because it throws off the count & value of your stock.