Just create the hole patter as a part... all you need is the PCB view... it will be stored in My Parts and drag it on as a part, you can have it with/without connector pins.
EDIT: Attached is a PCB part with no breadboad, schematic or connector pins/pads. You can look at the .fzp to see how it is done, All you need to do as change the pcb.svg with your hole pattern pcb.svg. You could also add an image in the icon.svg so you know what it is in the My Parts bin.
This was just a test circle that could be used as a pad or keepout pattern...
Circle Image.fzpz (1.6 KB)