Gale,
Technically speaking, the master drive is referred to as the first drive on the IDE Cable, on either IDE port. The first slot is the one in the middle of the cable and not the one on the end.
Secondly, you must setthe JUMPERS on both HDD's to be either "CS (Cable Select)" or the jumper on the drive connected to the first slot as "MA (Master)" and the second HDD as SL (Slave).
You can not use a combination of both. The system will attempt to boot from the Master disk first. If you have multiple operating systems, install the oldest one first.
You can then install the latest operating system on ANY partition you like, if you have hte hardware setup correctly as described earlier.