Ah, you are searching in Dropbox, not MR. It sounds like you need to contact a Dropbox forum, as while you are storing your ebooks there, the search is a function of Dropbox.
I would suggest just putting all your ebooks into either Marvin, MapleRead (or both) on your iDevice. Then arrange them to your preference, and eliminate the Dropbox search problem. You can use MapleRead CX for free with some limitations. Here is a link to organizing/searching in the three MapleRead versions:
http://www.maplepop.com/web/mr/overview.php#organize