Adding them as they are should produce a library that's totally integrated and not as indivdual folders, unless you have set each individual folder as a seperate source.
In the MB configurator you should only have 2 folders, unless you've set-up seperate profiles, being Movies and TV Shows, then within each of those you should add your folders eg
and so on and similarly so with TV Series.
This will then give a totally integrated library view.
TV Shows - are slightly different in that they have to be housed on the same dirve to show in 1 series, otherwise they will be listed individually - a restricition of MB I'm afraid.