Crikey! A lot of questions! I'm not very experienced on Linux, but I'll try and answer the bits that I'm fairly sure of, maybe someone elsa can come back with the rest of the answers, or correct me if I'm wrong.

First off, make sure your other stuff is backed up (or saved somewhere), this is just because if your not used to linux volume names/partitions it easy to get confused, but that apart:-

a). You need a swap partition, this is usually twice the size of the RAM your PC has. Everything else can be installed on the rest. This is the 'easy' setup.
b). It's knoppix-install for current versions of knoppix
c). The guide is at http://www.knoppix.net/docs/index.php/HdInstallHowTo
d). When you install, I think you get an option to use LILO (LInux LOader) this replaces the normal windows mbr - but check this one!!!! I'm not sure with two physical drives.
e). LILO is what I have (and W98SE on the other partition) GRUB I have no experience of.
f). Debian is hard/impossible!

By the way, when you do install knoppix plug in everything you want to use as the installer installs everything that knoppix autodetects. If it aint plugged in, your have to install it manually afterwards!

Stu.....