Using Subdirectories in Uploads folder

I have two sites, both use the Road Fighter theme. Only the one at The Soundsmith really has an issue. I have hundreds of audio files and images that would be far easier to work with if i could put them in subfolders under Uploads.

Is there a plugin, or can I just move the files? I I DO move the files, will I have to recode every page they are called from?

Thanks.