Im not sure what to do:

root@Machination:~#apt-get update
Get:1 http://kanotix.com sid Release.gpg [189B]
Hit http://kanotix.com sid Release
Hit http://kanotix.com sid/main Packages
Ign http://amd64.debian.net sid Release.gpg
Hit http://kanotix.com sid/contrib Packages
Hit http://kanotix.com sid/non-free Packages
Hit http://kanotix.com sid/main Sources
Hit http://kanotix.com sid/contrib Sources
Hit http://kanotix.com sid/non-free Sources
Ign http://amd64.debian.net sid Release
Ign http://amd64.debian.net sid/main Packages
Ign http://amd64.debian.net sid/contrib Packages
Ign http://amd64.debian.net sid/non-free Packages
Ign http://amd64.debian.net sid/main Sources
Ign http://amd64.debian.net sid/contrib Sources
Ign http://amd64.debian.net sid/non-free Sources
Err http://amd64.debian.net sid/main Packages
404 Not Found
Err http://amd64.debian.net sid/contrib Packages
404 Not Found
Err http://amd64.debian.net sid/non-free Packages
404 Not Found
Err http://amd64.debian.net sid/main Sources
404 Not Found
Err http://amd64.debian.net sid/contrib Sources
404 Not Found
Err http://amd64.debian.net sid/non-free Sources
404 Not Found
Fetched 1B in 1s (1B/s)
Failed to fetch http://amd64.debian.net/debian-pure6...64/Packages.gz 404 Not Found
Failed to fetch http://amd64.debian.net/debian-pure6...64/Packages.gz 404 Not Found
Failed to fetch http://amd64.debian.net/debian-pure6...64/Packages.gz 404 Not Found
Failed to fetch http://amd64.debian.net/debian-pure6...rce/Sources.gz 404 Not Found
Failed to fetch http://amd64.debian.net/debian-pure6...rce/Sources.gz 404 Not Found
Failed to fetch http://amd64.debian.net/debian-pure6...rce/Sources.gz 404 Not Found
Reading package lists... Done
W: Couldn't stat source package list http://amd64.debian.net sid/main Packages (/var/lib/apt/lists/amd64.debian.net_debian-pure64_dists_sid_main_binary-amd64_Packages) - stat (2 No such file or directory)
W: Couldn't stat source package list http://amd64.debian.net sid/contrib Packages (/var/lib/apt/lists/amd64.debian.net_debian-pure64_dists_sid_contrib_binary-amd64_Packages) - stat (2 No such file or directory)
W: Couldn't stat source package list http://amd64.debian.net sid/non-free Packages (/var/lib/apt/lists/amd64.debian.net_debian-pure64_dists_sid_non-free_binary-amd64_Packages) - stat (2 No such file or directory)
W: You may want to run apt-get update to correct these problems
E: Some index files failed to download, they have been ignored, or old ones used instead.

You need to change you sources. The AMD64 sources are no longer there they have been incorporated into the standard mirrors. Do a search of this forum and you will find several post regarding this.

I tried changing it as suggested in other threads, but I still get lots of errors. How do I know which sites to use and what I need in sources.lst?

Check out the sticky at the top of this forum and enter the lines exactly like they are in that thread. Also try removing the / between sid and the type.

The line should look like this:

deb http://http.us.debian.org/debian/ sid main contrib non-free

I get this after I changed it to the line you said

root@Machination:~# apt-get update
Get:1 http://http.us.debian.org sid Release.gpg [189B]
Get:2 http://http.us.debian.org sid Release [38.3kB]
Ign http://http.us.debian.org sid Release
Get:3 http://http.us.debian.org sid/main Packages [3069kB]
Get:4 http://http.us.debian.org sid/contrib Packages [39.7kB]
Get:5 http://http.us.debian.org sid/non-free Packages [37.0kB]
Fetched 3185kB in 11s (287kB/s)
Reading package lists... Done
W: GPG error: http://http.us.debian.org sid Release: The following signatures couldn't be verified because the public key is not available: NO_PUBKEY 010908312D230C5F
W: You may want to run apt-get update to correct these problems
root@Machination:~#

Try the following as root. Make sure you have sudo installed first.

1) open the Konsole, type su and enter your root password
2) then type: gpg --keyserver wwwkeys.eu.pgp.net --recv-keys 2D230C5F
3) then type: gpg --armor --export 2D230C5F | sudo apt-key add -
4) and finally: apt-get update

Ok thanks, now when I try to install things like below, or remove apps from kpackage I get errors about /etc/apt/preferences

root@Machination:~# apt-get install vlc
Reading package lists... Done
E: Unable to parse package file /etc/apt/preferences (1)

Try:

apt-get clean
apt-get update

if that does not work try searching the forums for "/etc/apt/preferences" to make sure yours has not been corrupted.

I tried that, and mine looks similar to other examples

Can you please post it?