Definitely have at least half (non-refundable) down to cover the cost of the materials. That's what I do for large orders, and smaller orders are completely paid for before I ever buy the materials or start the project. Also, be sure to put custom in your title and in your description. PayPal and Etsy won't make you issue a refund on custom orders, but it needs to specify that it is custom work.
Before you post the listing for it, be sure to update your policies regarding custom orders. You might want to read policies from other sellers who do custom work for some ideas.
Also, search for Custom Orders in the discussion threads of this team and the Questions forum team to see issues and suggestions regarding custom orders. Most custom orders are great, but there are some with problems. It is wise to educate yourself (by reading the trials and errors of others) before you commit yourself and your customer. The most important thing for a successful transaction is great communication between your customer and yourself, especially with custom orders. Good luck