Metadata columns can be created and associated to either sites or lists and can be further referenced by a content type. To create a new site column, you need to go to "Site Settings" and then "Site Columns" which is under the Galleries section. You then click "Create" and you'll be presented with the new column creation screen. Under "type" you will select Managed Metadata radio button. This column is now connected to the term store and you will have the opportunity to associate it with any specific term set in the term store. Only terms from the specific term set you select will be valid values in this column, thus a custom managed metadata column is more specific than the Enterprise Keywords column. Again, the Enterprise Keywords column can be populated with any terms from the term store.
In the example in the image above, the managed metadata column has been created and only terms from the WAND General Business Taxonomy will be valid values for this column.
To create a custom managed metadata column at the library or list level, you simply choose "Create Column" in the ribbon bar at the top under "Library tools" or "List tools" respectively.