Unapplied cash and deductions created from electronic receipts

We have three Companies currently setup...1, 3, and 5.  All cash receipts are received into a single deposit account under Co. 1, thus our electronic receipts file is loaded into the F03B13Z1 with Co. 1 as the default.  The receipts file may contain receipts related to invoices in either Co. 1, 3, or 5.  If the receipt is Co. 3 or 5 related and it has all of the necessary data to apply the receipt, then cash is recorded to Co. 1, an automatic intercompany entry is generated, and an entry to clear the customer's receivable is recorded on either