In Linguaplone, the one thing that you can’t translate is the portal itself. Hence if you have any documents or folders at site root, then they will be translated into documents or folders also at site root. It is easy to see how (especially with more than two languages) things can get very messy indeed.
However there is a way around this if you have your site address directed to a folder at the root of the portal, public_home, say (in my opinion this should be Plone default behaviour to stop user content from being scattered around portal tools in the zmi). You can then translate the folder and the translated folder will show up on the same level as public_home. (You can even translate some content inside the folder before you translate the folder and LinguaPlone will put the content inside the folder for you)
However, perhaps you want all content – including translations – to be inside the public_home folder for ease of maintenance. Well, after you translate the folder, you can go into the zmi, cut the folder and paste it within public_home. This doesn’t seem to have any effect on the links between original and translated folders, or on any content translated after you move the folder, and you now have all the content for each language inside their respective folders inside public_home.