Creating Mashups is a great way to give your visualizations a nice looking container in the form of a custom HTML web page.
Inserting custom-built extensions into your mashups, however, requires one extra step compared to standard objects.
First, custom extensions can be added to mashups just like any other object. However, the custom CSS file needs to be added to the HTML page of the mashup.
Let's assume both your extensions and mashups are stored in this folder (they will be by default):
C:\ProgramData\Qlik\Sense\Repository\Extensions
You'll need to add this line in the <head> of your MashupName.html file:
Adding a <script> tag for your extension's JavaScript file is not necessary because require.js will pull that in for you. As a final note: make sure you clear your browser cache after each change you make to your extension to ensure you're seeing the most recent changes to your CSS and JavaScript code.