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…
Any tips for what settings to change to prevent the destructive behavior you mentioned?
These settings can be useful in cleaning up badly formatted files, but should not be used carte blanche on all input files, especially those that don't have problems. You'll lose niceties like the first paragraph in a chapter not having text-indent, etc.
Generally it's better to use the "Edit book" feature on EPUB files and manually fix up the CSS if the styling is not to your liking. Converting with Calibre also hard-codes @page margins which overrides most e-Ink reader software's margin settings; so if I do end up using Calibre to convert to EPUB, I always have to edit it afterwards to remove these hard-coded margins in the CSS.