Manual Font Management Questions

Hi. First, thanks in advance for any advice. I appreciate it.
I've recently taken up comic book lettering and as such, have acquired a massive amount of fonts. I've tried a couple of the management software (Suitcase Fusion and FontExplorer X) and haven't been able to work with them the way I'd hoped. Furthermore, they all (including the native FontBook) sandbag my system and grind it to a crawl.
So, even though it's a giant pain and extremely tedious, I think I'll manually edit and remove unnecessary fonts to pare things down and organize them in apps like Adobe CS5. And group them. My questions are 1) can you have folders inside the font library folder the system draws from (for organization purposes)? I ask because there are none in there. 2) I've been working (I've already started with a small folder elsewhere) with a copy of the font directories. When I finish, would I just delete everything, then copy my altered version (including some renamings) into place (w/ or w/o folders -- tbd)? Or is there a proper way to remove and replace fonts than just moving to trash?
Thanks again! I (virtually) bow to your vast knowledge. (Pandering works around here, right?)
FiveByFive

Uh...  Kappy, I've got every font on my machine (except for /System/Library/Fonts fonts) in subdirectories inside the assorted Fonts/ directories.  This is a subset of FontFolio11 that we use for editorial:
cathy% ls -l ~/Library/Fonts/User_cathy_Library_Fonts/FontFolio11Pagination
total 8
drwxr-xr-x@  6 cathy  staff  204 Dec 13 16:04 Franklin Gothic Std
drwxrwxr-x@  7 cathy  staff  238 Aug 24  2010 HelFracAP
drwxrwxr-x@  9 cathy  staff  306 Dec 13 16:04 HelFracAP-Bold
drwxr-xr-x@ 25 cathy  staff  850 Dec 13 16:04 Helvetica LT Std
drwxr-xr-x@ 11 cathy  staff  374 Dec 13 16:04 ITC Berkeley Oldstyle Std
drwxr-xr-x@ 19 cathy  staff  646 Dec 13 16:04 ITC Century Std
drwxr-xr-x@ 19 cathy  staff  646 Dec 13 16:04 ITC Cheltenham Std
drwxr-xr-x@ 23 cathy  staff  782 Dec 13 16:04 ITC Franklin Gothic Std
drwxr-xr-x@ 11 cathy  staff  374 Dec 13 16:04 ITC Galliard Std
drwxr-xr-x@ 10 cathy  staff  340 Dec 13 16:04 ITC Legacy Sans Std
drwxr-xr-x@ 10 cathy  staff  340 Dec 13 16:04 ITC Legacy Serif Std
drwxr-xr-x@  7 cathy  staff  238 Dec 13 16:04 Melior LT Std
drwxr-xr-x@ 10 cathy  staff  340 Dec 13 16:04 Memphis LT Std
drwxr-xr-x@ 10 cathy  staff  340 Dec 13 16:04 New Century Schoolbook LT Std
drwxr-xr-x@  4 cathy  staff  136 Nov 29  2010 OCR A Std
drwxr-xr-x@  4 cathy  staff  136 Nov 29  2010 OCR B Std
-rw-r--r--@  1 cathy  staff   48 Nov 29  2010 fonts.list
Notice that they are ALREADY in directories!

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