Where is your problem?
See e.g. here the thread about albums being split up into subfolders by disc:
Even though this shows the way in the windows world, it also shows the underlying principles which are no different in the Mac world.
I think it is a question of workflow:
first send all the files to their separate folders which means that you first deal with folders where you collected files which really should be in separate folders.
And then you rename the folders.
What has happened to the original access problem? Has this been solved with the insights into file organization?