When scanning your collection, Ubooquity will include in its database all the comics and ebook files it will find in the folders you chose to share.
If you want to ignore some specific files, files types or folders, you can use an exclusion pattern that Ubooquity will test against each file to know if it has to be scanned or ignored.
One important thing to keep in mind is that the regexp you write will be matched against the full path of each file Ubooquity encounters (all the folders of the path and the file name).