You can do that with Ubooquity 1.6.0 (released yestarday).You have to configure Ubooquity to use a port different from 80, then choose a reverse proxy prefix and redirect traffic corresponding to this prefix and the port you have chosen to Ubooquity.

For instance, if your server name is "myserver.com", configure Ubooquity to use port 2202, set the reverse proxy prefix to "ubooquity" and configure your IIS/Apache/Tomcat to redirect all traffic corresponding to "myserver.com/ubooquity" to "localhost:2202". (prefix and port number are only examples, use what you want).

Im glad you like Ubooquity. :)

You can customize the theme ( tutorial here ) but it will modify the aspect of all the pages. There is no way to customize appearance of a specific subset of comics. And to be honest, I don't have plans to add such a feature.

I tried to reproduce the problem by adding a thumbs.db file to a CBR comic, but it did not work (the comic was still readable by Ubooquity).
I suspect that the removal of the "thumbs.db" file from the archive triggered a recompression by WinRar which fixed the problem (meaning that a simple recompression without removing the "thumbs.db" would have worked too).