Originally Posted by Konda

You don't have to ask your affiliates to send you invoices, it will be too much hassle for most and they will send their traffic elsewhere. You can create them for them (eg self-billing invoice). So for each payout you just create the invoice on your end and add them to their account next to each payout so they can download them if they want them. What they do it is up to them, but on your end you have all the invoices should you ever get audited. Many affiliate programs do it that way.