Completely new to xWiki I'm afraid I can't be of much help. But I think there is a clear thing: documents are in the database!
OK, I guess I just have to edit the document then, to ensure a proper formatting. But when I choose the "Edit" option it seems like it's only the content DIV I can edit. I guess I have to find the document in my filesystem and edit it from there. Problem is, I can't find that document. Where are the WXiki documents stored ? I cannot find them anywhere in [TOMCAT_HOME]/webapps/xwiki/