We use our own in house invoicing system which generates data in spreadsheet form (although it can be programmed by us to output to whatever required format).

We need an accountant to take this information and complete the balance sheets, year accounts etc.

Our system records each invoice/purchase number, invoices and purchases are then stored per month in its own folder. We place a marker in our software that is also ticked once we confirm the document is present to help prevent missing invoices so we know if theres anything to chase up.

Company programming company and experienced programmer.