[T-bird_se]

I did a quick test with a few movies

One folder with the movies
One movie with it's own folder including it's movie

Start Ember (no source set up yet) and go to tools menu, select sort movies in to it's own folder
Checked what's happen, and all is sorted to a folder with the same name as the movie file,the one that already in correct folder was untouched
Set up a source in Ember and let it scrape them

To clean up the folder and movie names (not necessary, just if you want it clean)
I use this setting for renaming, but everyone has his own ideas and likings
For movie folder: $T {($Y)} gives you Movietitle (year)
For file pattern: $T ($Y){.$S} gives you movietitle (year.moviesource)
Run the Bulk renamer

After that all is sorted and named nicely

So you can do the same yourself with a small testfolder before running on your main collection