Intended behavior with 2 departments

[Luke <..hidden..>]

Departments newbie here...

What is the intended behavior when orders with different departments set, 
are consolidated?

I sell various hosting and domain services.

Say a customer puts in an order for some domains, and I do an order.

Before that gets invoiced, he puts in a hosting order.

These are two separate departments, and would be reflected so on the 
separate orders.

However, I want only one payment, to save on CC processing fees.
I also don't want to confuse the customer with two invoices but one 
payment.

So I consolidate the orders, and invoice.

Only one department ends up on the invoice, and thus the payment is only 
associated with one department.

Which?

What else should I know about this?

Luke