The Mobile Theme won't take any elements from your desktop theme. It's a different theme, and cannot get any information from another theme on your site.
If you want an element like a custom template to be used on 2 different themes (like your desktop theme and a mobile theme like Jetpack's), you'll need to include that element in a plugin, since plugins are loaded regardless of your theme.
You can use the template_redirect function to load a custom template via a plugin:
http://codex.wordpress.org/Plugin_API/Action_Reference/template_redirect