Such a time I have had, getting my sixth book into the iBooks store! Finally, it's there! And it only took me over two months of trying.
That was sarcasm, by the way. My experience with this book was a good illustration of the difficulties in dealing with one retailer via another retailer. The folks at Apple don't make self-publishing easy, so I use Smashwords to get my books into the iBooks store.
In the past, Smashwords only accepted MS Word documents formatted with their specific styles. They had a program called the meat grinder that they used to create all the various formats they support (epub, Kindle, PDF, txt, etc). You uploaded your cover image and the Word file, and it took it from there. The books came out kind of vanilla, as far as style, but you got a valid epub file, and that was what made it possible to sell that book on the other retailer platforms. All the major online bookstores except Kindle rely on epub format.
If the epub book had an ISBN and made it into the Smashwords premium catalog (which meant it was well formatted) then it could be sent to iBooks. It sometimes took a week or two to show up but it arrived. Smashwords tries to be responsive to their authors, and when people asked to be able to upload epub directly, they made that possible as of the last day of of 2012. You can now upload an epub copy and an MS Word copy to Smashwords, and they will use the epub for all the non-Amazon online vendors. The book still has to say “Smashwords Edition” in the front matter, but otherwise it doesn't need to be different from any standard epub file.
Now iBooks has gotten pickier about their book covers. The cover image appears inside the book, as part of the epub file, and it gets uploaded as a separate file for use as on the store's web pages. Apple appears to have changed the rules about what resolution the image can be; too low or too high a resolution, and iBooks won't accept it. Smashwords must have realized this because when I uploaded an epub copy of my seventh book King of Trees, it told me right away that the cover image with the file was too low res. I got that cover artist to supply a different version and the book was delivered soon after and showed up in the iBooks store in a few days.
With TNG, though, it had passed epub review and gotten into the premium catalog with no trouble, and had shipped to Apple right away, but it never showed up in the iBooks store. I tried emailing Smashwords and they just tried to redeliver it for me. Still no TNG in iBooks. Eventually, I clicked the link to pull it from Apple, which makes Smashwords send a takedown notice, and once that was sent, I clicked Distribute again, but it would not ship to Apple! I emailed again, and this time the person investigated and told me the problem was the cover image inside the book was too high a resolution! I got the artist (different artist from KoT) to give me a lower res image and then had that re-inserted into the epub file. Once it was all straight, the book was there in a matter of days.
Victory at last!