I would assume an intra-company transfer would be better, with two sets of invoices you're doubling up the sales on the P&L. With an intra-company transfer you have a bank "loan" account on your primary and secondary account, one in debit, one in credit.. depending on which way the money flows. When you merge the reports they would balance each other out.
In general I think the two trading entities should be synced together through virtual bank accounts, so there's nothing on the P&L, everything is on the balance sheet.
Once you have sales invoices and purchase invoices to net things off, you're on the P&L. Also you're VAT registered right? So you wouldn't want any over reporting of sales or purchases, even though the bottom line tax calc may be correct if you over report your total sales or purchases this will distort your VAT return.