How do I correct a reconciled deposit that is matched to funds manually entered into the deposit instead of being matched to the actual payment?

I'm here to help you resolve this matter, @RockhoundingRanger98.

To rectify an incorrect transaction match, go to your bank register, and from there you can delete the transaction. This action will eliminate the mistakenly added deposit transaction and return the bank transaction to the For Review tab. You can follow these steps:

1. Go to your Chart of accounts. 
2. Locate the bank account where the transaction at issue is and click on View Register. 
3. Find the reconciled deposit and select it. 
4. Hit Delete.

You can click Yes when you're prompted twice that deleting the transaction will throw off the balance the next time you reconcile and will place the transaction back under for review.

Afterward, return to your Bank Transaction's page where you can either directly match the transaction to the payment or create a new deposit for the payment and then associate it with the bank transaction.

Here's how:

1. In the left menu panel, go to Transactions.
2. Go to the Bank Transactions.
3. From there, click the specific transaction.
4. Tick Match and it will prompt you to the accounts that you wish to match.
5. Click Match.

 After the matching process, let's re-reconcile the recently matched transaction. To do this, here's how:

1. Click on the Gear icon.
2. Select Reconcile. 
3. Click on We can help you fix it. 
4. Locate the transaction you've recently matched and mark it as reconciled "C" to "R". 

You can also refer to Step 4 of this article for the detailed steps: Fix issues for accounts you've reconciled in the past in QuickBooks Online.

Moreover, I am adding this article to help you properly categorize your transactions: Categorize online bank transactions in QuickBooks Online.

Feel free to post a reply if you have further questions regarding your bank reconciliation process in QuickBooks Online.

@RockhoundingRanger98 

You have a couple options:

1) Delete the payment that was applied to the invoice.  That will reopen the invoice.  Then, apply the manually-entered deposit to the invoice.

2) Reverse the payment that was applied to the invoice by creating a journal entry (JE) by going to New > Journal entry.  The JE should debit A/R (select the customer's name under 'Name') and credit Undeposited Funds.  Then, go to New > Receive payment and apply the credit created by manually-entered deposit to the A/R balance created by the journal entry.  Then, make a $0 bank deposit to clear the duplicate payment to the negative deposit created by the journal entry.