Calibre can transfer books directly to your Kobo using a Kobo plugin, just search the plugins for "Kobo". It will also update series info in your Kobo and will create collections on the Kobo based on tags you create in Calibre, though for some reason the series and collection data never goes the 1st time you sync to the Kobo, it takes a 2nd sync to push that data to your Kobo

I also saw a recent update by the author of Calibre that he is rolling the Kobo plugins directly into the application in a future release. Apparently the author recently switched to Kobo too, so the integration should only get better, but even with the plugins today I've had no issues syncing ebooks from Calibre to my Kobo, just right click the book and choose send to device main memory (or secondary memory if you have a device with a sd card slot).