It's by no means a stupid question. (But allways try to omit useless noise in topics, like 'newbie, question, please help' - that's stupid. About 95% of posts need help and have questions.)

The small answer is: "yes but no".

The long answer:
There are 3 problems I'm seeing:

a) Filepermissions:
If you install to a windows-partition (vfat, ntfs), they don't use the user-group-other rwx distinction, which might cause problems.
But you didn't tell us, that you're going to install it on a windows-partition - so you may install it to a ext3, reiserfs, xfs, whatever-filesystem.

b) Installation-procedure:
I'm mostly installing from tarballs, with 'configure, make, make install'. If you install from deb or rpm you have to read the manpages or find another anwerer.
My way would need me to specify a different install-dir:
Code:
configure --install-prefix=/mnt/mypartition/usr/local
c) Find the application on runtime:
If you boot from cd, without config-files from hd or usb-drive, the application isn't found by default, especially not if it is a plugin for mozilla.
You would have to write a small script, to have it found, or tell the browser every time, from where to take the plugin.

Note that this is only a sample:
Code:
mount /dev/hda4 /mnt/mypartition
export PATH=$PATH:/mnt/mypartition/usr/local/bin
All in all: If you use knoppix regulary, a hd-install gives many benefits. Buying an extra harddrive should be thought of.

Throwing away every windows partition is an alternative