Need SEO advice for sitemap

I have a large website containing link in the sitemaps but my new mobile version have completely different structure so its hard to use "canonical" (correct me if Im wrong)
How to build the new sitemap and overrank my desktop pages with the mobile ones.

Desktop site URL example site.com/category/subcategory/item.html
New mobile URL example site.com/category/subcategory/sub-sub-category/ (not all categories are coming to the url depends on what is chosen by the user) so it can be also site.com/sub-sub-category .


How can I prevent the two completely different structures causing more damage than good

Why do you have two different versions of the site? Hit me up on Skype and I'll try to help you.