I am 100% sure I understand the question - but I'll try to answer.
The video file for each game has to be named exactly the same as the game. Let's say you have Super Metroid for Super Nintendo (snes). If the Super Metroid game file is named "Super Metroid (Japan, USA) (En,Ja).sfc" then the video file HAS to be name "Super Metroid (Japan, USA) (En,Ja)" - otherwise the video would not load properly.
I would also keep video snaps in one folder (snaps), box art in a different folder (marquee or flyer, depending on the layout), wheel art (game logos - "wheels" folder) in a different folder etc. If you have a lot of different file types in one folder and that sounds like it would take a long time, you can go to the folder and organize by type and that will separate the image files from the video files - then you can simple grab all of the video files or png files (or whatever file type you need to move to it's own folder).
Idk if this answers your question - I hope this helps!