Normally inter-company transfer is a very sensitive area in accounting (usually related to transfer pricing) and hence are not allowed to be performed directly (meaning having entries in one journal in different company).  GAAP even have special section for Intercompany transfer.  So, in your case, it need to be viewed as 2 transactions happening separately of each other.  One is from a company to the partner (either supplier and/or customer), and both need to have invoice and payment.  Another is transfer of "asset" between the company.  Depending on which company you choose to handle the external transacations, the "asset" can be money collected on behalf of, or a intercompany sales.  Best is to check with accountant with knowledge of accounting rules in the jurisdiction where transaction occurs.