I downloaded a kernel image:
2.8.11 generic amd-64 kernel image
and
2.8.11 k8 amd-64
but I keep getting the error:
But my system uses a 64-bit AMD Athlon processor and a 64-bit MSI motherboard. The control centre recognises it as i686. I don't really know enough about Linux to re-compile a kernel so I'd like to get this to work, can anyone explain what's going on?

It looks like you have not used the 64bit installer and only have a i386 system installed. There is no way to upgrade to a 64bit system from a 32bit you need to do a fresh install. You can get the information on the 64bit port of Debian here there are links to the various installers there I would suggest using the Sarge one.

Thanks for the link. But is there a 64-bit installer included with the normal i386 Sarge distro or is it necessary to download the DVD torrent images? (May take a while at 4.3GB and 3.3GB) I'm currently downloading:
Sarge AMD-64 boot DVD
are these what you meant?

thanks again for the information

No there is no "official" installer for sarge it was decided not to include AMD64 in its release so they are just the ones linked from the page I posted. Depending on the type of connection you have (eg. not using dialup) I would just go with the netinst.iso on this page it is only 84mb and do the base install then do the rest of the install from the net. This will definitely save you the bandwidth in the long run there is not need to download 7.6 gb when an install over the net will never take that much you are basically downloading the entire archive at the moment.