This seems like a big deal, but it's really a simple issue.
I can say this because I've been running dual-boot Macs for over 20 years and I encountered and solved this a long time ago. It keeps rearing it's ugly head because it's not documented anywhere.
OSX and OS9 do not coexist peacefully on the same drive volume (remember volume - it's important) except for OS9 Classic, which is not bootable but just runs in a sandbox under OSX.
This is because they have similar but different directory files and when put on the same volume, they're not actually "aware" of each other.
Sooner or later under this setup (usually sooner) one or the other will write or delete something that the other one needs and you get what you now have.
This is easy to prevent.
1. In OSX disk utility, format a drive (yes, you gotta erase everything) making sure to check the box that says "Install OS9 Drivers"
2. Still in disk utility, partition the HD into two (or more if you like but at least two) volumes - one for each system.
3. Install OSX onto one partition using the OSX installer routine on the CD/DVD.
4. You can now install OS9 on the other volume in a few different ways, depending on what form you have OS9 in. You can:
A. Reboot from an OS9 install CD and install 9 into the other volume.
B. If your CD has the OS9 files expanded and available, you can just boot OSX and use it to drag copy the OS9 files from the CD.
5. If you only have OS9 as a disk image, use method B.
6. If you have more than one HDD in the machine, you can also put them on separate drives if you like since they're also different volumes.
However:
If the OSX version you have includes Spotlight and/or Time Machine you MUST immediately:
Go to the OSX system prefs for those apps and follow the instructions to prevent them from indexing, backing up or otherwise caring about your OS9 installation. Lock them out of OS9 - period. Otherwise, they will very quickly write stuff on the OS9 side that will cause problems in OS9, since it will be unreadable gobbledegook to OS9. Then, you'll get an ongoing war between the OS9 disk utility and the OSX utility and everything will soon go to shit.
This is what causes everybody to freak out and say you can't have the two systems on the same machine which is patently ridiculous.
That's it… finito, you're done. Enjoy your dual-booting Mac.