[G4] Opinions on partitioning strategy

[Technophobic_Tom at comcast.net]

In the past, under OS 9, I partitioned my drives so that the system 
files, applications, documents, and caches had separate volumes. My 
rational being that I only needed to backup the system and 
application files when major changes were made but I wanted to backup 
documents several times each week. I know...I was using DiskFit and 
could have selected which files to back up in particular sets; 
however, I also felt that there was less chance of the system or 
applications crashing and munging up the document files if they were 
on separate volumes. It's also nice to have clean, unfragmented space 
for images etc.

My son gave me his old MMD dual 1.25 400 including lots of recently 
installed applications and 10.4.8. I backed up the whole drive with 
Retrospect Desktop, added a HD, and partitioned that as follows: 121+ 
gigs, 10gb for DVD burning, 5gb for applications, 10gb for scratch, 
and 1gb for downloading, and 1gb for a redundant 9.2.2 boot volume. 
Then I used Carbon Copy Cloner to clone the original HD into the 121 
gig volume. All is working well.

Can I now simple copy the applications folder from the 121gb volume 
into the applications volume, pull all the applications out of the 
folder, then trash that empty folder, and replace the applications 
folder on the 121gb with an alias pointing to the new 5gb 
applications volume?
Are there invisible files that would be lost and not included in the process?
Do application preference files under OSX get mingled in with the 
system folder/files as they do in OS9?
Maybe I could use CCC to clone the folder. ????

Can I install 9.2.2 in the 121gb "system" volume now or will I have 
to uninstall OSX, install OS9, and then reinstall OSX so that I can 
run in classic mode?
I realize I can use the redundant 1gb 9.2.2 boot volume but mighten 
it be useful to have both options?

Most of my old applications will only run under OS9. How can I get 
them from my networked B&W, 7500, and IIfx and be sure all the parts 
are there?
Where do I put them?
Would it just be easier to reinstall them?
If so is that done in OS9, OSX, or does it matter?