It is not currently possible to separate the payments from one Cookiebot account into several invoices. It is also not possible to add more than one payment method to one account. One account will make one joint payment and receive one joint invoice.
However, you can add the various domains to separate domain groups so that you have one domain group per business unit (or per whoever in your organization needs to pay for those domains). On the joint invoice, it will be clearly marked what the price is per domain group and you can then handle the transfer of money internally.
As an alternative, you will need to create 3 separate Premium accounts in order to add a separate payment method to each account and to receive a separate invoice for each account and its domains.
Please also see: