It depends on where you're preparing your source doc. You can write your document in Word (where equation support kind of...umm...sucks), and save it as PDF. Or you can use something like LaTeX to prepare your document, in which case your PDF can look like it was professionally typeset.
When I was in college for a maths degree, I always used the MiKTeX platform (on Windows) to prepare any documents that had equations. Trying to coerce Word into behaving itself was just too dispiriting.
I've yet to find a good PDF to [epub|mobi] conversion. Even when there's zero complexity in the document. Seems like you lose most/all formatting or layout.
Hope this helps.
Last edited by JDK1962; 06-30-2011 at 02:31 PM.
Reason: forgot conversion part of response