Best way of setting up IS for companies that have accounts and pay later

We are set up fine for companies that pay by card up front and can see on the quote system how we can set it so that the customer can pay later, but in our case after we supply the customer (this is done by sending passwords online) we then would send an order or “invoice instruction” to our accounts department so that we can enter the sale onto the ledger and they can then be invoiced at the end of the month (through QuickBooks online).
We need (i think) some kind of email/notification to be automatically sent to the accounts department if the client chooses to tick the pay later option. Of course, this means that the person creating the order/quote knows that the customer has the option to pay later.
There is probably a simpler/better way of doing it but any suggestions would be gratefully received.