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If you intend to submit to amazon, the best way is to convert to EPUB and submit that, amazon sometimes throws a hissy fit if you send it MOBI files not created using its own software. Or if you want more control, convert to EPUB and then convert that to MOBI using kindlegen (from amazon).
If your book does not have sophisticated typesetting needs, things should just work. If it does then you will likely be in for a fair bit of back and forth.
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