I added a story to the Twilight folder, but there is a brief mention later in the story about Scootaloo being adopted by Rainbow Dash, should I also put it in the Rainbow Dash folder as well?

I would prioritise just the central characters when folder sorting, unless a story focuses on multiple families that is

2064116
uhhh what story?

2064309 Alright thank you.

2064489 Starbloom Chronicles.