HOWTO convert documents to Kindle / mobi format?
I didn't enjoy Calibre.  But then I realised that it comes with a bunch of command line utilities, and that made things easier for me.

Imagine you have a bunch of epub files.

for f in *.epub
do
  anytomobi --dest-profile=Kindle "$files"
done


That's the Linux command line to convert them all to mobi using the calibre tool.  Except I think the command line toold have changed name in the newest release.

Here's a website, from the Calibre pages, that claims to by a guide to converting HTML to e-book formats, including mobi.

http://amalthia.mediawood.net/tutorials/ebooks/index.html

This page seems most important for your question, it has nice screen shots for the settings used.

http://amalthia.mediawood.net/tutorials/ebooks/steps.html