Quick steps: Shop > Order Management > Settlements > Type 'Invoice' > Actions > Export
When Payment on Invoice is enabled it will show as an option to make payment at the checkout. The customer will be able to select Credit Card / PayPal or Payment on Invoice.
To view the settlements for orders that have been purchased through Payment on Invoice you will need to ensure you have selected the 'Type' Invoice.
These are available at the end of every day to download.
To mark invoices as paid follow the guide here.