I've automated this a bit by adding the following to my .bash_profile
Code:
#Create ePub file from exploded directory at CWD
# USAGE: zipub Path (shouldn't be under CWD) ie do zipub ../test.epub
zipub () {
zip -X0 $1 mimetype
zip -rDX9 $1 * -x "*.DS_Store" -x mimetype
}