Amazon has the lion's share of the ebook market with its Kindle platform, and the company has apps for Kindle, Android, Mac, Windows, and even your browser. That only works for Kindle format ebooks, though, and it turns out there are lots of other places to get ebooks.
Apple's iBooks is the best, in my opinion, but there's also Nook and its apps, as well as DRM-free epubs sold by third party ebook stores, some publishers (including O'Reilly), direct by authors, and by anyone making epubs with great software like Scrivener. Those DRM-free Epub files can be read in iBooks, too.
I've long made epubs of my own manuscript as well as any other long form fiction from other writers that I was editing. Make the epub, send it to Dropbox, open in iBooks, and edit away.
When Apple launched iBooks in Mavericks, however, those third party ebooks, including my own manuscripts, were nowhere to be found on my Mac. My iBooks-purchased books were there—including any notes and highlights I had made—but my other epubs were MIA, as demonstrated below.
iBooks in Mavericks – Where Are My Epubs?
When I went looking for answers, I found two ways to fix it. The first was to manually add those epubs to iBooks in Mavericks. According to this thread on Apple's support boards, that will cause them to sync between your iPad (or iPhone) and your Mac from then on.
That seemed sloppy, and it turns out Apple included an easy way to sync those files, and it's built into iBooks on Mavericks. In the File menu is an option called “Move iBooks from iTunes,” as shown in the image below.
iBooks in Mavericks File Menu
Select that option, and…that's pretty much it. After a moment, your non-iBooks epub files will appear in iBooks in Mavericks, as shown below.
iBooks in Mavericks – Now With More Epubs™
This includes any notes you made on your iPad, as shown below.
Editing Notes
The only thing I don't get is why this is even an option, why users much do this. If Apple is going to move iBooks to a dedicated iBooks app, as it did in Mavericks, it should sync your entire iBooks library out of the box without the user having to do anything.