Many times you will negotiate a static shipping fee per order per account. This may be a set amount e.g. $25.00 or it may be Free. Shipping override allows you to set that static rate for all order made by a particular customer.
You have negotiate with ABC ltd and agreed that they will get FREE shipping on all orders.
DEF ltd has agreed to pay $25 for shipping on every order, regardless of the products purchased.
Navigate to the customers account in the Admin and scroll down until you see "Shipping Override".
Toggle "Shipping Override" on
Set the amount you want to charge (0.00 to allow Free shipping)
Set the label in Checkout
Finally, add the label that you would like your customers to see in the checkout.