If you want to add books you don't purchase from Apple into your iBooks library, you have two main methods: sync with iTunes or sync with the iBooks app in Mavericks. Neither are very intuitive though. Cult of Mac points out that you can also send yourself an email with an Epub attachment.
All you need to do is send an email to yourself with the book as an attachment. Open it up on your iPad or iPhone, and tap the icon for the attachment. You'll get the option to open it in iBooks, where it will get added to your library. This method lets you skip plugging in your device, and it also works with most file formats.
How to Add Epub Books to Your iPad Without iTunes [Cult of Mac]