You reconcile accounts that have online banking the same way that you reconcile other banking accounts in QuickBooks, using the paper bank statement sent to you by your financial institution.
However, with online banking, QuickBooks helps you match the transactions from the transactions you download to the ones already in QuickBooks. By the time you reconcile, QuickBooks has already checked most of your transactions against the downloaded ones, so your records should be accurate and the process fast.
Usually, your downloaded transactions closely match the ones you enter into QuickBooks. Sometimes, though, your financial institution may process a transaction differently from the way you entered it into QuickBooks.
For example, suppose that you receive payments from five customers. In QuickBooks, you entered the payments, but not the deposit. when you download the deposit, a single transaction, QuickBooks has not way to know which payment transactions were in that deposit.
In this case, when you record the deposit, you'll select the individual transactions that equal the deposit total.
Working with online transactions in the Reconcile window
Troubleshooting reconciliation problems