Let's assume that the Net Term Add-on is integrated to your website.
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'.
Net Term Order Shipping Option #1
When you set up shipping rates in the 'Manage Shipping' section of Wholesale All In One, then these shipping rates automatically apply to the Net Term Orders and Regular Shopify orders based on matching customer tag.
Note: This method is compatible for both 'Draft Order' and 'Final Order' methods.
Net Term Order Shipping Option #2:
You can also set the shipping fee for the Net Term Order from the 'Drafts' ( not the 'Orders' ) section of the Shopify dashboard before sending an invoice to the customer.
Note: This method is compatible only with 'Draft Order' method but not with ''Final Order'.
Net Term Order Shipping Option #3
When there is no shipping fee added in the Net Term Order, and you send the invoice to the customer, then regular Shopify shipping rates defined under the path 'Dashboard > Settings > Shipping and delivery' automatically show to the customer during the invoice payment process.
Note: This method is compatible only with 'Draft Order' method but not with ''Final Order'.
Please look at the below screenshots for better understanding: 
When customer visits the Net Term Order invoice link received via email, then Shopify shipping rates defined under the section 'Dashboard > Settings > Shipping and delivery' appear on the checkout page, please look at the screenshot below: 
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