Cuddles: The one thing I don't know is how Kanotix (is that what you're planning to use?) will deal with a separate /boot partition. But my guess is, probably like it deals with a separate /home partition. (Read on...)

When you install it, it will format / (root) automatically. In other words, everything on / will be wiped out, and / will be formatted in your choice of file system (ext3, ReiserFS, etc.), before the files are copied to it.

It should automatically detect and use your existing swap partition.

You already know how you start the installer, configure it, quit, save the configuration, then go to /root and edit the installer's configuration file, .knofig. That's where you tell it where /home is (correct value inserted from what you gave):

Code:
# Here you can give additional mappings. (Experimental) You need to have the partitions formatted
# yourself and give the correct mappings like: "/dev/hda4:/boot /dev/hda5:/var /dev/hda6:/tmp"
HD_MAP="/dev/hda6:/home"
(Don't forget the slash / in front of "/home"! You won't get an error message and it won't mount it correctly.)

Then rerun the installer and perform the installation.

/home is not formatted, and the data on /home is not touched (which is why having a separate /home partition is such a good idea -- all the configuration data you already have there is used).

I'd assume /boot would be treated the same way (in other words, untouched), except in this case you want the new files copied to /boot. So maybe you don't want to add /boot to .knofig when you install; maybe you want to manually copy everything from the /boot directory that Kanotix installs on / to your separate /boot partition after you install, then edit /etc/fstab manually.