We use a sort of hybrid distribution. We format our own books and convert them for our online store. We upload directly to B&N through Pubit! and to Amazon through KDP because (frankly) our formatting is better and cleaner than what we get through Smashwords. All that said, the opportunity to get to Apple without having to either add yet another upload program AND buy ISBN numbers (which I consider idiotic for an eBook that will never be shelved, or bar-coded) - and to hit Sony, Kobo, and some other places without adding undue strain to our already overworked staff - totally worth it. It takes time to figure out what does, and does not work well at Smashwords, just like everwhere else, but we haven't run into an issue we couldn't get around (though we had some serious problems with one book and it's footnotes).
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