You can match the downloaded transaction with the one you already entered. This way, the downloaded bank transactions will be recorded in QuickBooks. Just make sure that your manually recorded transactions have the same amount, payment method, and transaction date with the downloaded ones.
Here's how:
Go to the Banking menu.
Locate the bank's blue tile.
In the For Review tab, select the bank transaction to expand the details.
Click the Find match button.
In the Match transactions window, enable the Suggested Matches feature.
You can also type in any details of the payment in the Search field to locate it right away.
Select the box before the Date column to select the match.