The Invoice Register breaks down what is invoiced by material totals, labor totals, special charge totals and sales tax totals, followed by the total invoice amount, the gross profit on the invoice, and finally the gross margin. However, any line items with a Product Code containing a Factor of 09, such as Freight, Discounts, etc., will only show as revenue, as any cost in the catalog will have no impact on the G/L.
If you want to job cost it, you will need to use the "Add Charges to a Job" feature in Accounts Payable when posting Freight Invoices, etc.
At that point, you can use the Sales Analysis module to see true Job Costs by using a Selection Level of Job Number.