As of now, the most obvious way (for me) to add emblems to a file/folder is to right click on it and choose "Properties" from the menu.
In this Properties window of files there is an "Emblems" tab.
In this tab there is a number of included emblems, however if you want to add a custom emblem to this list...you can't (from this dialog anyway). This is a bummer because it's the most obvious way (for me) to add emblems.
The interesting thing is, I didn't even know that I _can_ add emblems. While playing around with nautilus I discovered, that yes, I can add emblems (From "Edit>Backgrounds and Emblems" dialog in Nautilus).

Today, I wanted to do just that, and I looked at the obvious way to do it (right click on a file>Properties>Emblems>Add Emblem) However, obviously, this "Add Emblem" button doesn't exist.

So I'm proposing that you add a "Add Emblems" button to the file Properties dialog  (in the "Emblems" tab, of course).

-Gezim