Question not clear to me.
If you have one CC merchant account to receive credit card payments: Since the card deposit can only go into one bank account, the simplest is to write a check from the company the bank account is attached to to the company that actually should receive it paying the invoice for the customer who gave you the card.
If you are asking how to use one credit card for multiple companies, simply pay the proportionate credit card bill from the company making the charges.
