Since the show name and episode title are basically irrelevant (the scanner only looks for S1E1 or 1x01), I’d like to suggest this:
TV Show (Year)/
└─ Season 1/
├─ TV Show - S1E1 - Episode Name.ext
├─ TV Show - S1E1 - Extra Name-behindthescenes.ext
├─ 1x02 Episode Name.ext
└─ 1x02 Extra Name-behindthescenes.ext
