There are some questions un answered here.
Do you have more then one partition on the disks?
Did you connect the IDE1 disc to the IDE0 channel?
If you connect the IDE1 disc to the IDE0 channel you would not have to change anything. But if you connect the IDE1 disc to the IDE1 channel then you have to change the boot.ini file.
[boot loader]
timeout=30
default=multi(0)disk(0)rdisk(0)partition(1)\WINNT
[operating systems]
multi(0)disk(0)rdisk(0)partition(1)\WINNT="Microsoft Windows 2000 Professional" /fastdetect
Partition starts with 1 as the first partition
rdisk starts with 0 as the first disk on the channels
the thing you could try is that you backup the boot.ini file and then you connect both disks and then you edit the file and change the rdisk string to 1 instead of 0 and see if it will boot from the other disk.