First, in Disk Utility, highlight the whole drive, click on the blue Info icon above, see if OS9 drivers are installed...
|Name :||Newer Technology|
|Partition Map Scheme :||Apple Partition Map|
|Disk Identifier :||disk1|
|Media Name :||WDC WD50 00AAKB-00YSA0 Media|
|Media Type :||Generic|
|Connection Bus :||FireWire|
|Connection ID :||512384778896017|
|Device Tree :||fw/node@1d202e0bc0291/sbp-2@c000/@0:0|
|Mac OS 9 Drivers Installed :||Yes|
|Total Capacity :||465.8 GB (500,107,862,016 Bytes)|
|S.M.A.R.T. Status :||Not Supported|
|Disk Number :||1|
|Partition Number :||0|
If not your choices are erasing the whole drive & checking Install OS9 drivers, then installing OS9 & OSX again, hopefully you have the OSX Istall Disk & both that & the OS9 Discs are the right ones.
Possibly that App would run under Classic in OS9 under OSX 10.4.11, which would only require a working OS9 System Folder on your Drive, the CD version won't work.
In OSX, open System Preferences>Startup Disk, there you'll see available boot drives, also, holding alt key at bootup should show available boot drives, OS9 will have a Control Panel for Startup Disk.