iBooks Author is an amazing tool for laying out and publishing ebooks to iTunes. Unfortunately, the application creates books that are only readable on iPads. You trade off fantastic page design (via Apple's proprietary .iBooks format) for a much smaller potential reading audience.
When you want readers to be able to peruse your book on iPhone, you'll need to go with EPUB format instead. For all its faults, Pages still offers the best tool for creating compliant iTunes EPUB submissions that pass submission validation.
This allows us to use Word's collaboration and revision tools to produce a file that can be submitted directly to Amazon's Kindle Direct Publishing. For all that we yell and complain about Word, it's still the most powerful tool in our arsenal for manuscript preparation.
From there, we move to Pages where we mark out sections (Inset > Section Break, File > Save). This is an important step we've learned. Sections allow us to use images throughout our entire document. Otherwise, images are limited to 11 megabytes of unencoded data per section (or "chapter" in Apple's documentation). Pages omits those extra images during EPUB creation. Careful section insertion bypasses that issue.
From Pages, we export to EPUB taking care to check our primary metadata: publication name, author credits, and genre. Once exported, this is where a great new tool from Apple becomes part of our flow. Book Proofer (now available from your iTunes Connect author account) allows you to sync and preview EPUB files.
Just as iBooks Author lets you sync and preview iBooks files, Book Proofer does the same for EPUB. Drop a book onto the wooden shelf at the top of the app, select a device to sync to, and it opens in iBooks, ready for inspection. Unlike the iBooks Author version of this functionality, Book Proofer syncs with all iOS devices, not just iPads.
Be aware that you still need to have iBooks open on-device as in the iBooks Author version:
Once synced and open, we check for formatting issues, inspect our images to make sure they all made it through EPUB conversion, and perform a final sanity check. From there it's time to make any final metadata updates in Calibre before we submit to iTunes and begin our weeks or months long wait for approval.
While Apple's iBooks Author has received all of the attention in the press lately, the company also deserves a lot of credit and kudos for developing Book Proofer as a tool for working with EPUB files.