That's largely a matter of personal preference. I generally leave my frags on the plugs if I can find a convenient hole to hide the plug in. If not, you could carefully remove the frag from the plug and epoxy it in place.
You'd be cutting along the flat top of the plug, not through the coral.
A word of warning, most Zoas and Palys contain palytoxin. Under normal circumstances, this doesn't really affect us. However, if you disturb them too much they may secrete some. Definitely if you damage the polyps. If it gets on your skin, not a big deal. But if it gets in a cut or you rub your eyes or whatever, I understand it is extremely unpleasant.
All that being said, I imagine it's pretty rare to actually get sick from corals. If you can find a nice place to stick the plug, I'd leave it on so you can move it later if so desired. But that's just me!
Someone stop me! Please! But... not just yet...
55 Gal Tropical FW
55 Gal Mixed Reef