I loaded netrino onto my main box on a slaved hard drive. Did this
ruin the boot partition so that 2000 can no longer be booted? Is there
a howto to set this up?
when the system boots, the QNX loader will print
Boot Partition X ? X
at this point, you have a seconds to press a number that corresponds your 2000 partition. you can find that number out by running “fdisk” under QNX. Every partition is assgined a number from 1 to 4.
fdisk – No device provide
On boot, no matter what number I type in, boot partition comes back 1,
and only qnx boots.
The QNX bootloader might start QNX but I know that Win2k needs some specific code in the MBR. That was the reason I could not boot Win2k with LILO (although some people reported they could). 
So try to fix your MBR but first you should made a bootimage of your QNX partition (see documentation in link) an save this file to a partition Win2k could access (e.g. Floppy). Than boot with your Win2k CD to ?rescue console? (Sorry I have a german Win2k version and do not know the right specification) and fix your MBR with “fixmbrâ€
Disconnecting the second drive allows me to boot w2k. I fixed the mbr with fdisk /mbr using freedos. I also removed the qnx partition on the second drive. I made the second drive the primary drive on ide2.
I tried to follow the link, but have one question. How do you boot from second drive without loading the qnx bootloader into mbr? Since I could not figure out how to do that, I loaded the qnx bootloader into mbr.
After the second pass of the qnx boot, I was able to get the boot image to floppy using the mount and dd commands outlined at the end of the link ed1k.qnxclub.net/nt_qnx.html . I have copied the boot image for qnx onto drive c:. Using just the floppy disk to boot, I cannot get qnx to boot up. The ntldr gives me the option to boot qnx, but then the system ends up in the weeds.
Of course, I can continue to work like I am with the floppy to boot w2k and without to boot qnx, but this is awkward.
ed1k can give you a definite answer, but I seem to remember NTLDR can’t boot second disk.
On the other hand, you could try “grub”. You can have grub even if you don’t have Linux on the PC. You can have grub installed on a FAT partition. If your w2k is using FAT, you are all set, otherwise you can create a small (say 5M) FAT partition on the first disk. You can download the grub floppy image at uranus.it.swin.edu.au/~jn/linux/rawwrite.htm ).
Once you have the grub floppy, you can either use it to boot multiple OSes (w2k, qnx, etc), or if you feel floppy slow, you can install the grub onto the hard disk FAT partition. Just make a directory, say, \boot\grub, on the FAT partition and copy all files from floppy to this new directory. Then install grub into the MBR following mail-archive.com/bug-grub@gn … 06719.html
you could edit \boot\grub\grub.conf to create a boot menu … Learn more about grub at gnu.org/software/grub/