avid01 - Have you seen the
usage stats for calibre - the most popular version is 0.9.6 with 3.1%, the current version (0.9.25) is in 20th position with 2%. You don't have to upgrade if you don't want to, also see Preferences->Behaviour top left checkbox
If all you need is the converter, then you could just use the Command Line version of Calibre.
There's a thread somewhere in the Calibre forum that discusses the issue of annotation at length.
It includes a number of comments from Kovid Goyal. Search for annotate - last time I recall seeing the thread active was sometime last year. Maybe someone can has it bookmarked or subscribed and they can post a link for you.
I've given up on integrated, embedded annotations of ebooks - I just use evernote with links to the document, book, whatever in question.
BR