How to Add a Fee Based on Shipping Method
This documentation is for the WooCommerce Advanced Fees plugin.
With WooCommerce Advanced Fees you can easily add fees based on different conditions. One of those is based on the selected shipping method by the user. To setup a fee, first create a new fee or open the edit screen for a existing fee.
Click on the conditions drop down and select the 'Shipping method' condition from the list. When clicked, it will load the value field as a drop down, containing all registered shipping methods. Here you can select the shipping method where you want to add the fee to.
Shipping Rates vs Shipping Methods
There is a difference between shipping rates and shipping methods. If you followed the steps above, it could be you're not seeing the shipping methods you were expecting. If you use a shipping plugin they probably register one shipping method, and add multiple shipping rates at the checkout. Because shipping methods are pre-registered these are retreivable and can be chosen in the drop down, as opposed to shipping rates, which are not pre-registered and cannot be added to the drop down.
Setup a Fee on Multiple Shipping Methods
It could be you want to setup the same fee on multiple shipping methods. This can be done by adding multiple condition groups, each with a different shipping method (while keeping the possible other conditions the same).
In the screenshot below you can see how one fee can be applied to two shipping methods.