I appreciate you for reaching out to us here in the Community. Let me share what I know about customer payments in QuickBooks.
Are you using QuickBooks Payments? If yes, when processing ACH payments for the first time, they will be deposited into your account within 5 business days. The next time you process the payments, it would be a lot faster.
You can check the deposit status through the Merchant Service Center. Here's how:
Once you are ready, you may now proceed with reconciling your account are balanced and accurate. Visit this article for future reference: Reconcile an account in QuickBooks Online.
Let me know if you're referring to something else or if you need anything else. I'm here to help. Take good care!