Here's how I have my TOSEC folder layed out, a small snippet:
FTP Root -> TOSEC ->
Commodore Amiga - AMIX Files (v0.03)
Commodore Amiga - Applications (v0.20)
Commodore Amiga - CAPS (v0.04)
Commodore Amiga - Compilations (v0.18)
Commodore Amiga - Compilations - Applications (v0.01)
Commodore Amiga - Compilations - Games (v0.18)
Commodore Amiga - Coverdisks (v0.42)
Commodore Amiga - Demos (#-L) (v0.94)
Commodore Amiga - Demos (M-Z) (v0.94)
The above are sub-folders under the main TOSEC folder and then under each of the above listed sub-folders are the actual file-sets themselves. Each in their own .zip compressed format
Once you have a way you want to layout your files then I think even CLR should work for you. You can turn off the .zip compression option's in CLR when rebuilding. You just have to use the proper settings under the rebuilder button
