Use lots of symlinks:

mkdir /hd/usr/local/lib -p
cd /hd/usr
ln -s /KNOPPIX/usr/* .
cd local
ln -s /KNOPPIX/local/* .
cd lib
cp -Rp /KNOPPIX/usr/local/lib/* .

Then do your make install. You'll probably have to do this to a few different directories, but in the end everthing can work out fine.

Hope this helps,

- Ambrose