File all paperwork for expenses.
Include all items where the payment date is in the current year. The payment date is the day when payment was initiated, not the date it reaches the bank account.
You should also include items from the following year to be accrued. After the audit they should be moved from the current year folder to the next years folder (now the current one).
File in payment date order.
Check the paperwork is present for all transactions where possible.
Inter-account transfer confirmation sheets are filed in expenses and not in income.