Ok. I think I know what your talking about.
When someone request a custom order, They request it through your Request Order Button. You then work out the details of that custom order with your customer. Beginning with price. Now that's up to you, but most shops get paid 100% up front. I personally require 50% up front, payment in full upon completion of the order, before shipping.
Don't let that Custom Order button throw you, unless that's all you plan on selling?
Don't worry about the listing part...because really all you have to list is "Custom Order for XXXXXXX, with the set price you both agreed upon
so etsy gets their .20 cents.
Once you open your shop, you can enable that "Custom Order" button, and it will be on your left side bar too. ps It won't show up when you list your item...only after.
xo
Angela