Very simple step to sending an invoice to a customer for a diposit
Customer deposits can be handled as follows:
1. Receive the payment and leave it as a credit on the customer’s account. Then, invoice for it later and apply the credit to the invoice.
2. Use the + bank deposit and apply the deposit directly to the customer deposit acct.
3. (best method for invoices with sales tax): Set up an item that points to the account for customer deposits (a liability account). Use a sales receipt for the customer deposit.
Then later change your estimate into an invoice for the full sale and enter a line item for the customer deposit as a negative amount — this will remove it from the liability account.
Be sure to set this item as non-taxable. This way you will charge sales tax on the full amount in your final invoice.