You shouldnt have to.
When you change the jumpers on the drives, the computer and hard drives should be smart enough to know to load the master on the ide channel.
The OS has the boot.ini regardless if its master or slave.
This is a copy my boot.ini file. I only have one hard drive and one partition.
multi(0)disk(0)rdisk(0)partition(1)\WINDOWS="Micro soft Windows XP Professional" /fastdetect