DVD/Blu-Ray Extras - How to organise?

May I ask forum members how they organise any extras of their movies/TV shows?

I spent months ripping my entire Doctor Who (Classic Series) DVD collection and am thrilled that an app like Infuse for the Apple TV exists. With custom artwork my collection now sits proud and accessible whenever.

These rips had originally been housed in iTunes and therefore any metadata had been written within. The descriptions and titles carry over to Infuse but alas no mention of cast and crew (though this was the same in iTunes). I could rename the files and allow the app to grab metadata but I don’t like how the TVdB organises things. It would also mean I would have to put the shows into 26 seasons as opposed to how I currently have it: within 7 folders for each Doctor.

So for illustrative purposes I currently have it structured like so:

TV Shows > Doctor Who > 1 > 001 An Unearthly Child > 002 The Cave of Skulls.m4v
TV Shows > Doctor Who > 1 > 001 An Unearthly Child > 104 Comedy Sketches - The Corridor Sketch.m4v

Etc.

I would love to have detailed metadata for every episode and extra but I can’t seem to add a metadata .xml file like I can with movies. And I have tried this by creating a new folder for each episode file and ensuring all is named correctly. For example:

TV Shows > Doctor Who > 1 > 001 An Unearthly Child > 002 The Cave of Skulls > 002 The Cave of Skulls.m4v
TV Shows > Doctor Who > 1 > 001 An Unearthly Child > 002 The Cave of Skulls > 002 The Cave of Skulls.xml

So am I missing something? Can metadata be added manually to TV episodes? Am I doing this the right way or am I over complicating things? How do you maintain extras so they are with the matching episodes/films?

Is there a database of extras that Infuse could perhaps tap into with a future update?