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It would depend on which services you use. If most of your books are already in Amazon, then use that one. iBooks works equally as well, especially if you have iTunes gift cards you can use to buy content. Both will let you upload your own PDFs.
That will depend on you. Both apps are just reading apps with similar functions. Since most of my books have been purchased via the Kindle Store, it only make sense for me to use the Kindle App if I'm not actually reading my books via my Kindle Paperwhite because I can pickup where I left off on either.