The OSX install will format the drive for you; thats how I did it any way. If OSX installed with out any errors, try going out to Apple-Mac OS X-Developer and download the System Disk 3.3 utility and place it in your System Folder/Control Panel (this is a replacement for the Startup Disk panel...
I've got a second drive; however, it a SCSI drive and my main drive is the ATA-66 that came with my B&W.
Your going through too much trouble. Unlike PC's the Mac can boot from any drive. Just install the new drive as the slave and after installing OS X on it, you can use System Disk to select...
I have two hard drives in my B&W 300, so I installed OS X on the second drive (much easier then partitioning). The first time I installed I used the Unix format everything worked except the Classic environment. After installing a clean copy of Mac OS 9.0.4 on the first drive I still couldn't get...