Referencing the custom CSS from a publishing template

If you haven't already created a Publishing Template, see Working with publishing templates.
Using the Project view, copy your custom CSS in a folder inside the publishing template root folder (for example, in the custom_footer_template/resources folder).

Open the template descriptor file associated with your publishing template and add your custom CSS in the resources section.

<publishing-template>
    ...
    <webhelp>
        ...                
        <resources>            
            ...          
            <css file="resources/MyCustom.css"/>

Open the DITA Map WebHelp Responsive transformation scenario.
Click the Choose Custom Publishing Template link and select your template.
Click OK to save the changes to the transformation scenario.
Run the transformation scenario.

Your custom CSS will be applied as a final layer on top of any existing CSS rules and the output will reflect the changes you made.