Themus, have you tried Calibre's built-in epub editor? I find it the simplest, most convenient way to make tweaks to epubs and CSS sheets. It's what I use to delete embedded Charis fonts as well as xml files which can screw up formatting on my Sony reader, fix metadata TOC errors, and adjust margins and font sizes in the css file.
I used to use Sigil more, but ever since Calibre added the "Tweak Epub" feature, I only use Sigil if there needs to be extensive editing to the book's text itself. I think the tweak epub feature is one of Calibre's best assets.
Once Calibre "explodes" the epub for editing, you can use the excellent and free Notepad++ utility to do the actual edits to the epub's exotic file types (css, opf, toc, etc).
Last edited by PatNY; 11-30-2011 at 10:26 AM.