As i understand it, epistemology refers to your take on the nature of knowledge (e.g. can knowledge be adequately produced via the scientific method?) and ontology refers to your take on the nature of being (e.g. is there an essential nature than can be measured, or is 'being' merely the production of discourse, for example).
If you're doing post-structuralist work like i am, in a way i think its easier to debate such questions as I'm essentially going against the mainstream grain (i.e. my responses to the above 3 questions would be no, no & yes). But I'm still just working all this out, so other debates on this post would be welcome!