Finally there is more detailed information available how to create customized themes for Quickr (Domino). Especially the article on Developerworks contains very useful and detailed information about how the themes are working.
Customizing themes in IBM Lotus Quickr services for IBM Lotus Domino 8.1
Redbooks Wiki: Customizing Lotus Quickr 8.1 (contains also information for Quickr J2EE)
Customizing themes in Quickr Domino