You will need an account in each company's set of books called "due to/from <the other company> .  Set them up as current asset or current liability accounts.  

In the company that has the autowithdrawal, make a vendor invoice for the amount that belongs to the other company and post it to the due to/from account, no taxes.  Now you can show the payment coming out of bank in that company.  

In the other company set of books, where there are unpaid vendor invoice, make a negative vendor invoice for the amount that was paid from the other bank account, post it to the due to/from account, no taxes.  Go to the pay vendor bills screen and match up that negative invoice with the outstanding invoices that were paid out of the other company, for a net zero payment

Thank you so much for your reply!