I got all excited today, thinking I had found a solution to this conundrum... but I havent. It was in the Bookreader app
, from the Mac App store. I downloaded the Lite version which only allows one book at a time, and imported an already bookmarked book from itunes, but I guess the bookmarks don't persist in the import because they don't seem to be saved *in* the book. I thought they were, for some reason. Oh well.. I wrote to the dev and asked if it was planned for a future version because if it is, I'll have no hesitation in stumping up for the full version. Its a nice app.
 Crikey, the dev is very responsive! Already have a reply, within minutes of my query... here's the answer, and sadly not what one hoped for
The problem is that Apple's SDK doesn't allow BookReader to access iCloud data of other applications.
I hope in the future such access will be granted.
Naturally, I have asked him to consider creating a reader for iOS which would a) sync the bookmarks with the desktop reader and b) be a Stanza clone. LOL. couldnt resist.