How does the Shipping work with the Net Term Orders?
There are different ways to set up shipping rates for the Net Term orders depending on the selected Net Term Order methods such 'Draft Order' and 'Final Order'. CLICK HERE to read this article for better understanding.
How to reserve quantity by taking items out of the inventory when we are sending the draft invoices to clients?
When 'Draft Order' method is selected for the Net Term Orders then Shopify doesn't allow to reserve quantity for the draft invoices. However, You can change the Net Term method to 'Final Order' where you can reserve the quantity for the Net Term Orders.