The HD install in 6.0.1 seems completely broken to me, after having given it a couple of tries, I just gave up.
There are workarounds for installing Knoppix on multiple-partition disks, though. Here goes one of them, using Knoppix only:

1. Install HD in external USB cabinet, and format it. Create a 5-10 GB FAT32 partition as #1, a swap partition as #2, a /store partition and, eventually, partitions for other Linux installs. Here I assume that the USB-mounted ATA (not SATA here!) disk is /dev/sdc.

2. Format the actual partitions to be used,
Code:
mkfs.vfat -F 32 /dev/sdc1
, and, e.g.
Code:
mkfs.ext3 /dev/sdc3
Code:
mkswap /dev/sdc2
3. Use the 'Install Knoppix to flash disk' tool to install Knoppix on /dev/sdc1.

4. Mount the harddisk in the actual PC to run, and start up.

5. As root, mount the extra volume, e.g.
Code:
mkdir /store && mount /dev/hda3 /store && swapon /dev/hda2
. This should probably be put into an init script.

6. For eventual other Linux installs, the first patition will be handed as if Windows were residing there.

This worked fine on an old Dell Inspiron 8100, which I could only make boot from CD, floppy and HD. To have a more complete system to start with, I did not use the CD booting on that laptop to setup the disk (that ran awfully slowly, too!) , but transferred a complete Knoppix system w/4GB persistent disk image instead.

Works really well, and I will try to use this old laptop as a server. Have put in cards to get USB2.0 and work around a malfunctioning network chip.