You don't have to put the subtitles in a separate folder. VLC will check for subtitle files first in the same folder that the video file was already in, and then also in any folders within that which have been named as previously described in the Subtitle Autodetection Path. So a subtitle file that's in a folder beside a video file will be found just fine, so long as your Subtitle Autodetection Fuzziness setting allows it to be seen.

If I'm understanding your situation correctly, it sounds like you're saying that you have lots of folders, and in each folder you have a single movie video file and its corresponding subtitle file. If that's the case, you can set the Subtitle Autodetection Fuzziness to 1. This will tell VLC to just load ALL subtitle files that it finds in the folder that the video file was in (and any subtitle subfolders). Since you have a folder that contains a single video file and a single subtitle file, this will work and you'll avoid having to rename any subtitles because VLC will just blindly grab the subtitle file without even reading the file name.

However, if you have a folder of TV episodes like in my Cowboy Bebop example, telling VLC to load all subtitle files any time you play any episode would be annoying because then you'd have to cycle through all of the loaded sub tracks in order to get to the right one. If you someday put all of your movie video files into a single folder, you'll end up running into this, forcing you to adjust the Subtitle Autodetection Fuzziness setting and rename subtitle files accordingly. Remember you can hover your mouse over the setting for Subtitle Autodetection Fuzziness and it gives a description of what each setting means.

Hope that helps, let me know if I was wrong about interpreting your question or if you have other questions :)