I'm here to share further details about managing payment transactions in QuickBooks Desktop (QBDT), @DVFFJohn. This way, you can keep your data accurate and updated.

Before we start, I'd like to verify how did you record the payments (Check or Deposit)? If the payment shows as available credit while receiving payments when changing the account to Accounts Receivable (A/R), then do it to avoid duplicates.

However, if the above process didn't work, you can delete the payment. Then, receive the invoice payment and deposit it into your checking account. For the complete details, please see this article: Record an invoice payment.

Also, to further guide you in organizing your cash flow, and tracking sales, receivables, and profitability accurately in QBDT, I'd recommend checking out this article: Get started with customer transaction workflows in QuickBooks Desktop.

Keep me posted in the comments if you have other concerns about managing payment transactions in QBDT. I'm always ready to help. Take care, and I wish you continued success, @DVFFJohn.