Basically, you need a kepub not an epub. The few times I've played with kepubs, I've used either the KoboTouchExtended plugin to convert the epubs to kepubs on the fly to send to my Kobo ereader or I've used an external program called kepubify to convert epubs to kepub.epubs and added them to an separate calibre library before sending them.
My personal preference is epubs since I don't like some of the differences in the ACCESS NetFront renderer compared to the Adobe RMSDK renderer. The only time I use kepubs is for the few epub3 ebooks where they make use of epub3 features that cause problems for the Adobe RMSDK such as fixed layout epub3 ebooks.
If interested, you can check the following link for more information:
Kobo ePub Guidelines.