Be very careful in checking if Knoppix is really seeing the content of the hard drive. It could well see directories, but not be able to find the actual data when that data spans across to a second or third drive. If you do have true hardware raid it would be the first time that I ever heard of it included on a motherboard.

As to installing Knoppix, my best advice is don't. Knoppix is really intended as a Live CD or DVD, and things go wrong when it is "installed" (and even more so when additional software is then installed). Particularly for someone who describes himself as a Linux novice, I think that you would be much better off installing Debian or some other distro that is intended for installing to hard disk rather than Knoppix. I would suggest doing a net-install of Debian"unstable" or "testing". I know of absolutely no software that comes with Knoppix that you can't simply install in Debian with a simple apt-get, so I see no reason to fight with known Knoppix issues when a Debian install is straight-forward.