v3.4 of the Kobo app is now available in iTunes. They've made a number of improvements:
• Add books in ePub to your Kobo library from Mail, Safari or add them to iTunes and sync them to iPhone, iPad or iPod Touch.
• Add PDF documents to Kobo from Mail and Safari or add them to iTunes and sync them to iPhone, iPad or iPod Touch.
A friend tipped me to this on Twitter. He also noticed that when you add ebooks this way they won't be synced to your account. He recommended using Dropbox instead. And if they have DRM, the new methods won't work (even if the ebooks were bought from the same Kobo account).