@Sven Groot: I used a separate piece of software (I can't remember the name) that held your references and did something like a mail-merge to add (and format) your citation list at the end; so you hat to tag your citations in text with the ID of the citation in the software package.  In the end it wasn't that bad.

I did think about writing something myself and marketing it, but didn't have the time in the end.

@evildictaitor: I only had two simple formulas in the entire thesis, so the old formula editor was fine .