That's really the best way to do it, since you have to tape scrap film to the negs and punch it. The carrier is pretty big (for 4x5 film) so you'll need a good chunk of scrap film to be able to punch it; the pins are further apart than 6cm, too. When I do 6x7 negs, I take a piece of film and cut a 6x7 opening in it and tape the neg on all 4 sides, seems to keep them nice and tight. I use red litho tape.
Then throw in that you can get a little nuts with masks, and you'll want to save your print maps and notes with each neg. I make "storyboards" vs. print maps, when you start using several masks per print, you almost need to rehearse the order - the little comic-strip things I make are WAY better than marking up a print, it orders each step - like you may add a mask but need to softly burn in just part of it, stuff like that. (Pic below).
Other tips if yer interested! Get a bunch of 4x5 wax paper envelopes from Adorama/etc, and store each mask in its own envelope to keep them from scratching each other. I stick all of those in a 5x7 manila envelope, and that and print maps goes into a manila "job jacket" in a waterproof file box. I tape a scrap print to the jacket, easy to find when you want to reprint. Everyone's different, may be some good ideas there for your own workflow.
Label the masks with a black or blue sharpie between the punch holes - it's easy to get out of order or stick a mask in the wrong way, but if they're labeled you'll know from being able to read the labels. Some masks may be really thin, and it's hard to sort them out in the dark. And a red sharpie's invisible under safe lights. this is helpful if you reprint months later, too.
OTOH, red sharpies are your pals here - fine and regular points, to tweak masks and dust spot and so on. You can wipe them off with a q tip and alcohol if you screw it up.
I've had trouble getting SCIM masks to align perfectly, so I make them soft (duratrans or matte mylar between the neg and litho film when contracting) and use them as burn masks - works great and exposure are more controlled. Really dense litho negs always seem to need some spotting, fine point sharpie to the rescue.
You'll be handling negs a LOT, way more than you usually would. And as you dial in a mask, you don't need to punch every one - think of them like test strips. So you'll be sliding little scraps of litho film under your neg, so take real care not to scratch them. Your negs will be handled like a (insert non-PC euphemisms about ladies with loose morals in sailor's bars here!!). I lay out kim wipes to set negs and masks on and be careful sliding test film under the negs. This saves a ton of film and time as you dial in mask exposure and development, I'm often cutting almost postage stamps of litho film until I get the right density.
You may have a dozen dust-attracting surfaces in one print, between the glass carrier and the mask, so air blowers, humidity, a zero stat gun can all be handy, don't lean over the negs and so on. Even a face mask if you have a beard. An illuminated magnifier on an arm is killer, you turn the negs about until the light reflects back, and dust just leaps out at you - an artist brush and you can sweep them away.