For shelves / collections take a look at either
Kobo_Shelves_and_Collections or the slightly older version
Quick Guide to Shelf Management with calibre 0.9.1 & above (Touch / Glo / Mini /Aura)
Using calibre I strongly recommend installing
[GUI Plugin] Kobo Utilities and configuring it to do things like backup your Kobo database
Remember the use of metadata plugboard to help with including series info in the titles as send to Kobo. See either the Shelves and collections link or the dedicated thread
Techniques to use plugboards, custom columns and templates
If you decide you want to use Kobo's other reader (ACCESS vs RMSDK) install
[Device Plugin] Kobo Touch Extended Driver. Don't worry about the unsupported nature of this.
I would suggest ignoring the hacking aspect of the Kobo device for the time being; don't bother with the various patches / hacks available for it at first, and don't feel the need to install either of the 3rd party eBook reading mods (KoReader and CoolReader) yet.