Once you have the item on the PO screen just change the REFERENCE not the GL box on the edit view of the item to the GL that is for shop supplies and that will then put the value to that GL instead of putting stock into inventory.
To set a specific shop supply fee to a specific customer, access the customer file in question and press F9. From there follow the directions in the Image below.
Needed to change the % shop supplies setting to L on existing tickets, so walked her through using the % [shift] & 5 on the WO and changed the "A" to "L"