Calibre is great, if you configure it properly. By default, converting books to another format will change the layout! Destroying the original formatting by default is unacceptable behaviour to be honest, so user beware. For Kindle, I suggest using the KindleUnpack plugin instead; which can extract the EPUB file embedded in the AZW/KF8 format file losslessly for use with EPUB based readers without having to worry abo…
Converting ebooks doesn't destroy formatting unless you convert to a formatting-limited format like mobi or rtf as an intermediate step. kf8 and epub are roughly equivalent.
KF8 is a proprietary wrapper around a regular EPUB file.