To reconcile a bank account, you must fill in the reconciliation header and lines, and correct any necessary lines. If the contents of the Statement Ending Balance and Total Balance fields are not equal after correcting lines, then you must apply entries. For example, you may find that a single transaction on the bank statement corresponds to two separate bank account ledger entries in the program. In this case, you must apply these two ledger entries to the reconciliation line for the bank statement transaction.
Open the 
Bank Acc.
Reconciliation window.
Select the line with the entry to be applied (you probably entered this line while you were correcting the lines).
Click Apply Entries.
Click the Applied field on the entries to be applied to the reconciliation line.
Click OK to apply the entries.
In the Bank Acc. Reconciliation window, you will notice that the Difference field on the line is now 0.00.
Applying Two Bank Statement Transactions to One Ledger Entry
Handling Erroneous Bank Statement Transactions
Posting Transactions Recorded by the Bank Only