Knoppix on portable USB-HDD

I am currently using Knoppix on a USB-Flashdisk which is working just great. However the usage is limited by a image size of 4G caused by FAT32 formatting.
My aim is now to put Knoppix on a portable USB-HDD featuring a larger encrypted image. So far I couldn't find a howto. To summarize:
- there is no problem to put Knoppix on a bootable USB-HDD using 'Install KNOPPIX to Flash disk' option but it uses FAT32, so container size is limited again
- I had some issues to put Knoppix on USB-HDD using 'KNOPPIX HD install' since it was deleting the MBR on the internal HDD and didn't boot later on. Anyhow I don't believe it would solve the issue as it doesn't feature an encrypted home directory.

any other ideas?