How to change the indexing of the site and its alternative version in google?

Question

Google

Once I read and regretted the article that when creating an alternative version on a subdomain (in my case, mobile), you must immediately add two versions to Google webmaster (and Yandex).
The result was that in the large version of the search there are two versions in the issue:
site.com and m.site.com I was
looking for information on this subject, I did not find anything useful.
Looked at site.com and m.site.com coverage. I made a comparison and was surprised that Google prefers m.site.com more, and site.com is simply thrown out of the search at a slow pace.
Although, immediately after the creation of m.site.com, canonical is placed everywhere on site.com.
Site.com is tagged alternative version of 640px to m.site.com.
Tell me how to solve this problem?
Perhaps you should remove the m.site.com version from Google Webmaster?