Hi,
ok, I better understand your confusion now.
Changing yUp to zUp 'as a whole' in CityEngine is currently not possible. CityEngine works and stores everything in cartesian coordinates, in yUp. That's the way it was designed and that won't change in CityEngine soon.
So since you have GIS data, you may not know that in ArcGIS 10.2, we provided a GP tool to have the geometries created directly in ArcScene (no import in CE > Generate > Export to ArcScene). So that may be an alternative to work entirely in zUp. Though there's a hotfix needed for 10.2 and CityEngine 2013 to actually create the RPKs ( Rule Packages ) to feed to the GP tool. So that's upcoming. Also, the GP tool is really stripped down in it's interface (only 1 start rule allowed, no attr changes possible to run the tool. This was done for simplicity, though I doubt it was a good decision.)
So this means for you, it's best to just 'think' anything in y being height and xz being the horizontal plane. ALL the tools inside CityEngine work that way, ONLY the Navigation Display shows a 'live recalculated' info status in a standard zUp GIS way.
> Currently no way around this.
Let me know if you need more details / inputs !
Matt