Hi !
1]
Yes, you can host your files also on your own server.
2]
There's no API available yet of the WebGL viewer, but you can e.g. edit a few colors and exchange the images used to personalize your viewer. Though there's no tech-support for this. Some other threads are about this topic on the forums.
read on here :
http://forums.arcgis.com/forums/205-CityEngine-Import-Export
e.g. the stricky threads.
Lemme know if there's more questions !
Matt