Issues check was deposited for wrong amount

I appreciate you reaching out to the QuickBooks Community, @Morgan_s.
 

I understand the importance of accuracy in bank transactions during the reconciliation process. In QuickBooks Online (QBO), we're unable to match two downloaded transactions to a single existing entry. 

Let me guide you on how to manually change the reconciliation status in your bank register. 

First off, we'll have to exclude the transaction in QBO. Here's how: 
 

1. Go to Bookkeeping and select Transactions.
2. Select Bank transactions and choose the appropriate bank account.
3. Click the For Review tab.
4. Tap the checkbox of the transactions to exclude.
5. Hit Exclude.

After that, we can manually change the status of the transaction in QBO:
 

1. Select Settings and tap Chart of Accounts.
2. Find the account you want and click View Register.
3. Click the Payee Account. 
4. On the ✔ column, change it to C. 
5. Hit Save.

Check out this article if you wish to print your reconciliation report: How do I view, print, or export a reconciliation report?

If you have further concerns on how reconciliation works in QBO, let me know by commenting below. I am here to help. Stay safe!

@Morgan_s 

If this was just a check (New > Check), then reduce the original check by $9, issue an additional check for $9 to the same Category, and list EFT as the check number.

If the original check was a bill payment, reduce the original bill payment by $9.  That will leave $9 due on the bill.  Then, pay the $9 bill and use EFT as the check number on the bill payment.