A straight calibre installation has everything needed to handle the Kobo devices. The extended driver can be used if you want to send books as kepubs instead of epubs. The Kobo Utilities adds lots of handy things.
If the collections are not being created, it usually means the configuration is wrong. The most common reason is that on the "Sending books to devices" page of the preferences, metadata management is not set to automatic. But, have look at
Quick Guide to Shelf Management with calibre 0.9.1 & above for full the details on the configuration.