Originally Posted by Altivo
It may help if you tell us what version of Calibre, which model of reader, and what operating system is on your computer.
Using Calibre 0.6.x or 0.7.x on Linux the Kobo Ereader (Wi Fi version) shows up in Calibre without doing anything special. I don't use Windows or Macintosh with Calibre, so I can't tell you about those two systems.
I use Windows 7 with Calibre and have no problem. When you connect, your Kobo asks you to continue, after entering yes, Windows then asks you to open folders etc. [At the last resort you can transfer them across into the folders]. Then just highlight a file that you want to transfer from Calibre and the "transfer to main memory" - then Calibre usually connects and marks all of the books in its library that are in the Kobo.