Should I be receiving payment manually when I deposit a check for an invoice? QB is then seeing deposit and crediting my customers for a 2nd time, resulting in a credit
I can share the steps on how to record the payment you've received from your customers, @vince3.
When you receive a deposit from your customers, you can simply enter the payment through Bank Deposit. Once the deposit is updated, you can apply it as a credit to the invoice. This will make your records accurate and avoid errors when you reconcile your accounts later on.
You can go to your Bank Register to update the Deposit entry:
Go to the Accounting menu and select Chart of Accounts.
Look for the account you deposited the payment to, then select View Register.
Find and click the deposit and tap on Edit.
On Bank Deposit screen, scroll down to Add funds to this deposit, then find the fund you need to edit.
In the Received From column, search and choose the appropriate Customer name.
In the Account column, search and select Account's Receivable,
Select Save and Close.
To apply the credit to the invoice:
Go to the + New button and choose Receive Payment.
Select the Customer's name and add the Payment date.
Under Outstanding Transactions, select the Invoice you need to mark as paid.