Hello,
You can use the Shipment cost document account assignment settings to post the Freight costs directly to Expense accounts. As required by you Customer accounts will not be touched.
Also in SAP Standard transportation and Shipment is the only way to capture Freight costs after Delivery / Sales Invoices are created. Any other method will be very crude and difficult to track and generate reports. One of the methods already highlighted above is directly posting to GL Accounts.
Thanks,
Jignesh Mehta
