Dear Chiara and members of the list,
Unfortunately not all the texts of Perseus have been converted to CapiTainS guidelines for the moment. To have only texts which pass the guidelines, you'll have to download the release.tar.gz that are available in each given repositories such as
https://github.com/PerseusDL/canonical-latinLit/releases/download/0.0.12/release.tar.gz . There is two part of the server, one is the CTS API (and some other APIs like a DTS skeleton), the second is the UI which has no XSLT whatsoever but allows you to browse at least :) It should be possible to provide one but I would really need some support on making the app-building mores streamline before going there. If any of you has some spare time ;)
As for the directories, they are loaded together but not as "browsable" collections . They are just merged. Any other system would make it quite more complex for the end user at the moment :)