You don't. All pads and holes are terminals, whether they're electrical or not. It's how PADS works. Just add them.
Like Dave said, it is standard practice to have more terminals on the decal than on the schematic symbol; say 16 pins on the symbol and 18 pins on the decal (footprint) if two are mounting holes. If you want a hole in the board for a component, it must be a terminal.
If you want the mounting holes connected to a net, such as chassis ground, then you need to add the terminals to the symbol also and connect them on the schematic.