In the Atlantis Word Processor Blog you can find information about making changes to existing eBooks in the EPUB format (including eBooks generated by Atlantis):
http://atlantiswordprocessor.blogspot.c ... -file.html
http://atlantiswordprocessor.blogspot.c ... adata.html
http://atlantiswordprocessor.blogspot.c ... rgins.html
There you will find a download link to a new free utility called tweak_epub.