Okay... all's good
In the simplest case, the stack (probably best if glued up with some of repositionable spray glue) is placed on the work surface (if smooth enough) and the piece to be cut is placed on top of the stack, over the holes layer. Lightly pressed down flat, the vacuum should take hold and the entire stack, along with the workpiece, is sucked down onto the work surface... hopefully under the tool head of your CNC
Few notes on this.
I did glue mine with spray glue. One thing to watch for is warping. Weight it down with a large board while it drys and will want to warp otherwise. Also once it's built store it flat (and best with weight on it) as I've found it wants to warp if stored upright or even just sitting.
I want to make a new one with a wooden frame that it glues into so it will stay flat and I can position it easier. In fact I may just make the two lower layers out of wood to make sure it stays flat.
I don't really even have to press mine down except in the corners when it starts to warp. Even with a tiny $20 super cheap shop vac it makes enough vacuum to hold the pad to the table with nothing on top - it's not a super strong grip so you can still reposition it but it's strong enough that the weight of the vacuum hose won't pull it out of position.
And once you put your workpiece on top - it's not going anywhere. If you want/need to reposition anything you either have to pull the plenum out or lift the workpiece and let some vacuum out. (which is the other reason I want to add a wooden frame - so it can act as a "stop" to hold the workpiece aligned with the left and bottom edges more accurately.)
The top layer of the stack, the "holes" sheet, becomes the sacrificial layer and will eventually have to be replaced... but that should be many sheets down the road. A sheet of DTFB from the local dollar store, 15-20 minutes cutting the holes in the sheet, and you should be back in business
I've cut more foam than I can track (probably 2-3 cases of it at this point) since building my vac table and my top sheet is still going. It's getting pretty worn in some areas (for some reason the lower left corner seems to get more use than the rest even though I usually cut full sheets...I guess I just tend to put more small parts down there when I lay out sheets!) and I'm starting to think about replacing it....but not in any rush. And due to the warping I'm experiencing with the whole thing I'll probably just remake all of it rather than replace just the top sheet. (I did use reposition-able spray glue for the top sheet so it can be removed...but I kind of suspect it won't come off cleanly enough to be worth replacing.)