One thing you might consider is looking at making an epub by hand. (not all the time, but once or twice to familiarize yourself with the internal structure) I find it has helped me a lot in figuring out issues I've had.
This site has a great tutorial in my opinion.
http://www.jedisaber.com/eBooks/tutorial.asp
at the moment though it appears to be down. If it doesn't come back it is archived at
www.archive.org