I LOVE custom orders and that's really where I have the most creative fun, too! I started out not asking for deposits, and thank Goodness, never had a problem....but, when the orders got more & more costly, I created a listing that SAID it was a deposit, and spelled out the terms of the order and how much would be due upon completion. Once the deposit listing was paid, I'd start production (or purchase supplies, as the case might be), then when I had the item ready to ship, I'd create the Balance Due listing, including the shipping (and insurance, if necessary) & send that link.
Once that final listing was completed, I'd ship the item(s). No complaints so far! Good luck!