Boot Magic Problem

I have an AMD Duron 900mhz processor on an ABIT KT7A Mother Board. I have 2 hard disks, a 40 gb and a 12 gb. The Larger disk is set up as the Master and the 12 as the slave. I have Windows 98 on the 40 and Windows NT on the 12. When I try using Boot Magic, which came with my Partition Magic Software, the default OS (Win 98) has no problem booting, but when I try to boot the 2nd disk which has windows NT it won’t boot. Should I have both hard drives set as Master? Any help given is deeply appreciated. Thanks