To avoid the dual-drive-lost-partition-map problem, it is best to disconnect the OS X drive during install. However, this means you will not be prompted to add OS X to the yaboot (bootloader) configuration.
As a work around, you can either:
a) Boot from the YDL Install CD #1 with the OS X drive attached. Proceed until you get to drive partitioning and record (on a piece of paper) the partition that contains the root volume for OS X. Exit the installer, detach the OS X drive, reboot from the Install CD #1 and proceed to install. You may manually enter the recorded info during Install (/dev/hdbx, where 'x' will be the partition number) when prompted to edit the boot configuration.
... or ...b) Modify the yaboot.conf file by hand post-install, and re-run ybin.
"a)" is actually simpler.
This HOWTO was prepared by Kai Staats, Terra Soft Solutions, Inc.