I've never used the online conversion of the ebookwise bookshelf. I've always used the
Ebook Publisher from eti and impserve which is part of
ebookutils.
Ebook Publisher lets you convert html to imp format books and impserve will let you use a directory on your own computer as your online bookshelf. Almost all ebook formats can be converted to html not just lit but lit and mobi seem to convert the best, even then sometimes the html that you get has to cleaned up before it can be converted to an imp book that is readable.