Custom fees are applied separately to add ons and packages, here's how you can apply them to add ons.
Custom Fees
Custom fees are applied separately to packages and add ons. This is to ensure maximum flexibility allowing different fee's to be added if necessary. One add on can also have a different custom fee per location it is assigned to.
How to Add Custom Fee's to Add Ons
Add Ons -> Specific Add On -> Assign -> Scroll bar right -> Edit Tax and Fees
From here, you can create your custom fee for your addon per package it is assigned to to ensure maximum flexibility.