I recently published our first devotional book for my website. . .http://www.knittedtogetherbygod.com
. I published it through Smashwords because of the simple fact that you can get through many more options than with Amazon. I know for fact that Smashwords is still having problems working with Amazon. I talked to both Amazon and Smashwords about the problem of getting my book on there. Needless to say, I have remained unpublished on Amazon. For many reasons, with my book a ministry book I didn't want to charge my customers one single penny for the book, I have remained with Smashwords because with them you do not have to charge anything for your book if you do not want to.
With Amazon, you must use the KDP route or go through the Createspace route to be published underneath Amazon. I found this very annoying. They will only allow your book to be free for a period of time but not indefinitely like Smashwords. . .that is why I did not use Amazon at all. I'll wait until Smashwords can work out their differences with Amazon before I charge my customers for the book. It doesn't make sense why they do this with the new formatting, it used to be a lot simplier to use, now it's just complicated. So I strickly use Smashwords because of it's ease and distributions options. I hope this helps you and make sense as to what I'm saying here.
I prefer Smashwords over Amazon any day! Just my personal opinion on it, Amazon makes it really difficult to be on there. You have to charge at least .99 cents which isn't a lot so it really depends on what you can and cannot do as to which format you pick. For me, Amazon wasn't a option.