Set up an Account (not a Category) and transfer the amounts spent to that account. The account should be classified as either bank, cash or credit card to allow reconciliation.
On receipt, transfer the cheque amounts to the account. The account should then be reconciled to confirm correct receipts.
Expense any disallowed or amended items to maintain the correct balance on the account.
If there are lump sum allowances and/or mileage payments, credit them to either a suitable income category or against an appropriate expense.