When you receive a customer payment, you can deposit it directly to your bank account or to the Undeposited Funds account.
If you choose the Undeposited Funds account, you'll need to create a bank deposit:
Once you've deposited the payment, it will now affect your account register. This should also show when you reconcile the said account.
You can use this general article to know more about reconciliation in QuickBooks Online: Reconcile Hub.
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