What we've done in the past is setup navigation categories in the Categories app. Start out by adding a new category called Navigation. Under Navigation add the following:
These will be used in your repeaters to set specifics on which pages appear in which navigation structure. Assign the respective categories to the respective pages.
In your page template, add a repeater for the main navigation and set the properties of the path, page type, category (Main) and transformation. Now add a second repeater for the mobile navigation and set the properties of the path, page type, category (Mobile) and transformation. This should get you what you're looking for.
What you might want to consider though if you have a large content tree is caching both navigation items by setting the properties in each of the webparts so they don't query the whole site each page load.