I don't know any Mac OS X but had a quick google.
It sounds like you have boot problems and it looks like following command may be useful:
/usr/sbin/bless is used to set volume bootability characteristics for Macintoshes. The command can be used to select a folder on a mounted volume to act as the blessed system folder, and optionally update Open Firmware to boot from that volume. It can also be used to format and setup a volume for the first time. Finally, it can be used to query the folder(s) that are blessed on a volume. Try the following (non-destructive) commands:
% sudo bless -verbose -info /
% sudo bless -verbose -plist -info /
So if you can, try and run this command and in particular to check the second drive boot setup.