Hmmm...if it has tagging, I've never used it (with Calibre either). I organize via the folders I save the fic into. ::shrug:: works for me, YMMV.

Ads and sidebars seem to go away for the most part. Sometimes they get turned into a list of links at the bottom of the document (or top), but I ignore those. Art is tricky. Sometimes the art is displayed, sometimes it's ignored (or an X marks the spot where the art would be). I'm not sure that it's the conversion that does that, though; it may be a function of the website I'm saving of how I save it.