For what it's worth (my opinion that is!), I am not a fan of the way Boxsets/Collections are now handled.
To be blunt but not trying to be rude to the developers, the Web-Based Metadata manager is slow and very difficult to use which makes setting up Collections difficult.
I can't see it ever replacing MetaBrowser.
I also believe that having all my Movies (1200+) in a single folder without collections is messy at the very least.
Still, cudos to the developers and supporters of this product. Everyone should appreciate all the hard work and support of this great product.
While a flat folder full of movie files is a supported structure, I think, it isn't something I've ever seen recommended. The most common recommended folder structure is a folder for each movie. The folder has the same name as the movie and both typically include the production year in the name. For example:
\\movies\hd\Movie1 (2010)\Movie1 (2010).mp4
\\Movies\hd\Movie2 (2013)\Movie2 (2013).mkv
The change is that to create a collection you used to create a folder with a [boxset] tag and put the movies inside it like this:
\\movies\hd\MovieCollection [boxset]\Movie1 (2010)\Movie1 (2010).mp4
\\movies\hd\MovieCollection [boxset]\Movie2 (2013)\Movie2 (2013).mkv
Now it is recommended you use the first approach for all movies and just create the collection through the web UI.