Before I provide you with my suggestion, I would reach out to your accountant. They can ensure you with what's best for your books and give accounting advice.
I recommend creating an Invoice for the full amount and let your customer send partial payments. This can help you with Inventory and keeping track of the customer's balance. Here's how to record the deposit after creating the Invoice:
Go to the +New button on the left-hand menu, then Receive Payment.
Select the name of the customer from the drop-down menu.
Choose your payment method.
Enter Reference no. and Memo if applicable.
Under Amount Received, enter the amount of the partial payment.
From the Outstanding Transactions section, pick the Invoice the payment if for.
You can either deposit the money to your checking account or the Undeposited funds account.