Yet another way is to manage your own libraries. You can copy an existing footprint from either another library or a project to your own library, and then modify the footprint to look as you like it (and save it of course). You do this once for each footprint, and then you can use that footprint as many times as you like in other projects.
But what is this $(REFERENCE) you are mentioning:
If I add some unconnected footprint directly to a PCB in a project (With PCB Editor / Place / Add Footprint [O], then it shows up as REF**
Paulvdh - The reference designator shows up in a duplicate copy "$(REFERENCE) which lives on the FAB layer. Of course, it does not affect the Gerber or the PCB, but I prefer to just not have it getting in the way.