QB Issue Resolution:
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1) Set up a other currently liability account and call it customer deposits.
2) Set up a new service item and call it DOWN PAYMENT or something similar. In the income field of the item template, use the new customer deposit account.
3) Invoice the customer using the DOWN PAYMENT item.
4) When you invoice the customer for work actually performed, create a progress invoice and at the bottom of the invoice enter the DOWN PAYMENT item as a negative amount which reduces the amount that customer owes you and applied their down payment to the invoice balance.
Resolution for Issue 'When using estimates, what is the best way to invoice for a down payment?' available: Yes (Solved).
Source: Intuit Community forum.
When using estimates, what is the best way to invoice for a down payment?: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.Support for Balance
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