Hello Matt
You could set-up service Items for Freight and additional charges in Bydesign as well.This is the recommended process to handle taxable and non-taxable freights in sales processes, you need to create separate service items for freights. Freights can then be treated as taxable or non-taxable, depending on the master data of the service product.
Regarding the Non-Stock flag, if you don't activate the logistic area for a material, then it will be considered as Non-Stock. Once all the logistic areas are activated, then it will added as To-Stock item.
Kindly let me know in case of further queries/clarifications.
Thanks
Parveen Kumar