Ugh ... music management is an enormous pain and unfortunately, not easy... BUT there is one way you might consolidate everything into folders slightly easier than manually, it's a bit sneaky, so see if you can follow along. ;)
First, grab a copy of Serato DJ. You won't be using it to DJ, but it has a cool feature to make this whole thing easy.
Next, dump all your music into it. You could grab your entire iTunes folder, Music folder, external hard drive, whatever - just drag and drop everything into Serato.
If you want to separate your music into ANY kind of structure, this is the time to do it. Make crates based on any criteria you want to use to divide the music (whether it be by year, genre, BPM, etc).
Fourth, decide where all your music files will live when you're done. Is it a new external hard drive? Go to that new home and make folders to match the crates you've just created in Serato.
Finally, within Serato, select all the tracks (CTRL+A on PC or Command+A on Mac) and drag and drop that list into the new folders. This will make a copy of all that music from that list into the new location! Genius, right?
The actual FINAL step you can take to delete your tracks from your hard drive, regardless of where they live -- go to the "ALL..." part of your Serato library and select all tracks, then hold SHIFT and press delete. This will not just remove them from Serato, but delete them from the library.
If you ever plan to use Serato again, simply drag those folders back into the Serato crates and presto.