I am setting up my manufacturing central and want to be able to set the low stock threshold to the free to use items rather than the total in the warehouse. How can I achieve this please?
The low stock threshold is part of the WooCommerce core, not ATUM.
With the Product Levels add-on you can configure the "minimum threshold", "selling priority" and "available to purchase".
If you need more info regarding the BOM stock control in Product Levels add-on, you have documentation here at the forums:
I hope this helps.