Xero have no plans to introduce automated "landed-cost" calculations (where freight / customs / duties / extraordinary sales taxes / licensing are included as Cost of Sales for particular Items). The best they offer in this Feature Request thread is advice on how to do 'adjustments' appropriately - search for "Official Xero Reply".
To work that with our integration: your Procurement Freight Account Code should be 425 (http://support.innoventsoftware.com.au/solution/articles/124292-export-settings ) so the integration will put all those amounts into that Expenses account.
After the Purchase Order comes through, manually adjust in Xero by adding a bill, and expensing the freight to 425.
In your surrounding business process, it might be least painful to match up the freight and peripheral costs at the point of selling the item, when you can zero them out against the sales invoice.