Huh. So just dragging it from the object window into the render window would allow me to create one that's not visible in game?
That would be the jist of it. You are basically just creating a new one of that type. Like, for instance, if you made a new vault, you would still just drag and drop the vault static parts into your map; you wouldn't have to create an entirely new one for each piece you lay down. Normally you create an entirely new 'object' when you want it to behave differently than the original one. (Hope I explained that right... it's easier to just do than explain for me usually =p)
Anyhow, for the XMarkers, yeah, you just can drag and drop one from the list on the left into the window and plop it down. Then if you need to use it and reference it in some way, you can double click the one in the render window and edit it's information (for example, for the ref id you might put "xMyMarker", then later in a script or ai package or what not, use it for a reference).
In doing this you are only changing that specific xmarker, not all of them in the game. It is basically that the stuff on the list in the left are blueprints, then the things in the render window are separate creations - all made, following the same blueprint, but each able to be individually altered. If, however, you double-click it, click to edit the 'base' item, and change it - that alters every single one.