I wrote: Once the
drive is self-booting you should be able to make it "slave" or "master" in either channel, assuming the BIOS supports that.
Correction/clarification: you will still have to run lilo each time to change the device designation (/dev/hda-b) which is (or at least was at one time) hardcoded by writing it directly into the kernel image. This is one of the more kludgy aspects of the kernel booting process. There was a tool called rdev which also does this, but I think it's been deprecated.