Your store can have many different URLs (locations), for example your store can be running on Facebook, your website, embedded in your blog, etc.
Canonical URL sets meta canonical URLs in your store to point to the primary domain of your store so that Google, Yahoo and other search engines would correctly associate content of your store running from different website URLs (locations).
Meta canonical is generated automatically in your store taking in to account canonical url that needs to be setup if your store is running from multiple locations (websites).
To setup your store canonical URL, navigate to SETTINGS -> My Network -> Connections
In the bottom left corner you will find Canonical URL setup section.
From the drop down menu, choose the url you are using as your primary store location (canonical url drop down will list your store url at eez.io along with custom domains that you have pointed your store to)