The MBR is _not_ a partition, just the very first 512-byte block of your HD. I think cfdisk is the clearest partitioning tool to use. Delete all existing partitions from your hda, then create a swap, a root, a home. Mark them with the correct type. I dunno about the kanotix installer, but it should then run mkfs/mswap according to the way you've marked your new disk slices, and proceed from there.