The general rule, for any scenery is: you usually put the more localized scenery ( which is *supposed* to be more precise ) on an higher level than the more general scenery.
Something like X-Class, being a landclass, should probably stay between the MS default sceneries, and the addon airports.
I'd probably put it higher than UTX (don't know about GEX, does it come with a landclass ?), because we think X-Class is the more accurate landclass available for the US so, you might want to use the UTX improvements in roads/rivers/coastlines, but with the X-Class landclass.