I make it paying for guitar build very pretty straight forward and easy. Payments are always split into the following to make payment manageable:
20% on completion of body
20% on completion of neck
20% on completion of the guitar
This makes it easy for you to finance the guitar over the period of time during which the guitar is being built (on average a guitar takes 9 to 12 months to complete currently).
I take payment via bank transfer or credit card via PayPal (receipts can be provided as well).
Of course, you’re more then welcome to make larger payments or spread the payments after the deposit over a period of time that suits you (monthly, two monthly, etc) to make it easier for you.