The collections on the Kobo devices are stored in an internal database. When you add a collection using the devices UI, it adds to the database and each book in the collection is another entry. The KoboTouch driver in calibre can create or remove those database entries when it sees the device. If you want to do it yourself, then you just need a little SQL knowledge.
Personally, I use calibre to manage my ebooks. That way I have a copy of everything in a known place. When I connect my Glo, I can see what is on the device. Then I can manage exactly what is on the device though calibre. As I maintain my collections in calibre, they are automatically maintained on the device. Calibre also gives me the ability to change formats, fiddle with the metadata and covers and edit the epubs if I want to fix something (and I do as I am fussy). Plus I record the reading status, my rating and maybe some other things. And of course, I just like to play with it. And yes, I do actually read the books from time to time
