The simplest and easiest process requires you to post all invoices as per normal invoices - there is no need for any fancy spreadsheet calculations.
1 - The initial Inventory invoice
2 - The Intercity transport invoice - using clearing account
3 - The local transport invoice - using clearing account
4 - The Summary tab
5 - Amend the Inventory invoice for the Freight-in + contra line (Note - the Freight-in line Qty must be blank)
6 - The Summary tab