Normally additional cloop files are numbered after base KNOPPIX(3.9gb) file.
This is when the newer cloop file KNOPPIX2 contain only new applications.
General process is to cloop`pify the persistent file content (this process is well known)

What I am trying:
1. Install minimalistic debian(cli only).
2. Add all your application needed, for me, its most likely the ones not in knoppix.
3. upgrade to same kernel as knoppix.
4. Cloop`pify the whole system.
5. Drop is as KNOPPIX, before renaming KNOPPIX->KNOPPIX2

Cons:
Lots of extra/duplicate files get in cloop.
Pros:
I can create a small standalone specialized installs like rescue/diagnostic,
then drop it in current knoppix or use separately.

Well. tried the above and it works, though some minor tweaking needs to done before.

What I was thinking was if knoppix had option like:
knoppix_list=KNOPPIX,KNOPPIX3
This would allow to switch my system or mix match application during booting.

Another neat thing would be to have a base KNOPPIX(150mb cloop), and other cloops just application.