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You'll want to create a liability account to track the retainer's total amount from your customer. Then, create a retainer item so you can track the amount on your invoice. Let me walk you through the steps.
To create a liability account:
To create a retainer item:
Here's an article that you can check out for detailed steps and information: How to Record A Retainer.
You can match your QuickBooks transactions against your bank, please check this article for future reference: Match and Categorize BankTtransactions in QuickBooks Online.
Post a reply to this thread if you need further assistance. I'll always be around to help.