Hi Suzanne.
1. The best way to work with "aditional cost" in the raws is with Material Ledger and the Actual Cost Component Split. With this function, you can also rollup the freight and show its share in the finished product.
2. Also for COPA, ML is the best option because your COGS is valuated at Actual, and you dont have price diff account. Also, you can see the Actual CostComponent Split there, and see the share of the adicional cost like freights.
3. Other option to change indirect cost is Template Allocations, this is a mix between costing sheets and Activities. You can see an example of templates in the following post.