At the end of the established period the company should make the Bank Reconciliation operation in the Free Accounting application.
Bank Reconciliation is an operation of comparing your records of a bank account with the bank's records, as shown on the Bank Statement issue, of the same account for the definite date.
Bank Reconciliation statement is a paper your company receives from the bank every month.
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Banking button on the Navigation Pane, select 
Bank Reconciliation.
Reconcile Now button.
Master Transaction Ledger under the 
Company in the Navigation Tree
or select it from the Company | Master Transaction Ledger.
All the checks that were reconciled become cleared (the tick appears in the Clr column ) in Free Accounting.