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managing several companies AR and AP

I manage several companies on quickbooks online. The problem I am having is some of our clients know us as one name even though we bill them from company A they pay company B. My question is when this happens what do I do (besides trying to get the customer to pay the right company-I have tried that). 

example: we invoice client XYZ for 15k from company A. they Pay with a check to Company B. Company B does not have this client. We have to deposit the check in Company B's bank then transfer the money to Company A. How do set this up without creating income for Company B and making both PNL's reflect the ritght income. 

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Re: managing several companies AR and AP

The 'cleanest' way to deal with this problem is to ensure that Bco issues a separate matching check to Aco for every transaction and notes on the payment who the true Customer/Payor is

Then Aco can record it as an invoice receipt from Customer.

In Bco you would record a deposit into a liability account "Dueto Aco" and then issue a check to Aco coded to the same account - with the memo indicating the original Payor