Its not a mess, you just want it done differently, for which there is no program (that I know of) that will scan tosec files and "group" them.. sorry
My tosec is laid out the following way:
Bippy's lame attemt at a directory tree/structure 
FTP ROOT:
-= MY MISS LISTS =- ; What I miss, tosec and Goodxxx
-= Requests =- ; Requests that users make
Arcade ; Mame etc...
GoodXXX ; Good sets
Nintendo SNES 0.999.5 ; Not complete/up to date
Non Grouped ; Non-tosec/Goodxxx
Acorn ; Archie, BBCM, Electron etc
Atari ; 2600, ST etc..
Commodore ; Amiga, C64 etc....
TOSEC ; My Tosec sets
-= Misc Smaller Sets =- ; Small sets rar'd
Acorn ; Guess whats in here, look below
Acorn 8 Bit Roms (0.35) ; Dat name holding roms
Acorn Archimedes (0.33) ; and again
" " " " " ; All the acorn dats
Apple ; Apple sets
" " " " ; Guess what.. all the sets
Atari ; And another folder range
" " " " ; All Atari sets, grouped
Commodore ; Okay here we go!!!!
Commodore Amiga ; Amiga sets in here
Commodore Amiga - Amix Files (0.03) ; Amix files here
Commodore Amiga - Applications (0.20) ; Apps
anyway you get the idea, its only a mess if you let it be... but I see what you are saying, and as for putting each in its own folder, why not just turn on ZIPPING that way each file goes in its own zip, and WinUAE can read the zips
(Bloody formatting aint working
)