Use Disk Utility on the OS 10.3.9 drive to reformat the other hard drive as a Mac OS Extended volume and be sure the "Include OS 9 Drivers" option is checked. You should have done this, when formatting the OS X drive as well. When booted to the OS 9 installer disk, you should be able to choose the newly-reformatted hard drive as the destination disk. I'm curious about your use of (2) hard drives in a 350 MHz B&W G3. Are these ATA/IDE or SCSI hard drives? Those early B&W G3s (with the poorly-programmed IDE controller) don't reliably support master/slave configuration of dual drives. Additionally, those models don't reliably support large IDE hard drives (20+ GBs and larger). Most of those G3s shipped with a very small IDE hard drive or a 9 GB SCSI hard drive. Those of us who owned one and wanted to install larger/faster hard drives, eventually installed Ultra ATA-100/133 PCI controller cards to handle them. If you're using SCSI hard drives and they share the same bus (ribbon cable), be sure that the addresses don't conflict with each other.
Check out this Knowledgebase article, as it explains the importance of having "OS 9 Drivers" included on the OS X hard drive. When you're booted from the OS 9 hard drive and wish to restart from the OS X drive via the Startup Disk control panel, the OS X drive won't be recognized. Unfortunately, the B&W G3 doesn't support the "Startup Manager" feature for selection of the boot volume at startup.
Thanks Jeff, I followed your recomedation and it seems to be working. I am not a 'computer guy', I forget the reason I have 2 hard drives in the ole bugger, I have a lot of old mac software and adobe software that I want to utilize, my 10 year old version of appleworks 5 has more capabilities than my newly bought I work, ditto for my old Adobe pagemaker software. I labled the second HD, a maxtor 38gig, os 9, and was just going to unplug the other hard drive, and let the kids use that compter just for reports and stuff.
thank you. Neil