This is how LMCE is supposed to work. When you go to Videos, for instance, LMCE will show you all of your videos (directory structure is pretty much ignored).
However, you media can have attributes set for them - performers, genre (action, comedy, etc), you name it. This is the approach to take with LMCE. Orbiter have functions to sort by performer, genre, etc - so in the end the functionallity that you are wanting is there, you are just going to have to set up attributes for your media using the web admin.