Thanks for adding further details, @Annjay. I got your back to ensure you'll be able to record and categorize the invoice payment correctly. 

In QuickBooks Online (QBO), you can simply delete the wrong bank transaction and perform the manual update to download the latest entry.

Follow along below to get this done right away:

1. In your QBO company, go to the Banking menu.
2. Select Banking tab and click the account where the transactions is allocated.
3. Next, navigate to the For Review tab.
4. Check the box of the transaction with the wrong amount.
5. Select Exclude or Delete.
6. Choose Yes to confirm the action.

After that, manually update you bank to download the latest transactions. Here's how:

1. Select the Banking menu.
2. Then, click the bank account where the transaction belong.
3. Next, select the Update button.
4. When finished, check if you'll now see the correct entry.

Once everything is fine, you'll now ready to record the invoice payment and categorize it in QBO. 

Let me know how the steps goes. I'd love to know updates about this. If you have additional concerns about recording bank transactions in QBO, feel free to post again here. Have a good day.