Reconciliation of accounts is a process of reconciling your current balance in the budget software and information obtained from the bank statement to ensure that these amounts reconcile. Perhaps you have already created and entered some transactions in the program, but they are not yet reflected in the bank statement. Or, perhaps, the bank adjusted transactions in your account and you have not reflected these adjustments in the program.
To reconcile an account, you need to open the Reconciliation dialog (Tools - Reconciliation), select an account, date and enter the amount specified in the bank statement, so that the budget program can compare it against its own data. If the program says that the balances agree, click Reconcile.