those PCI cards should work fine in both OS 9 and OS X, I have a similar RAID version in my G4 and can boot OS 9 and X with it. If you are getting a new larger drive and want to boot into OS9, the OS 9 System Folder must be on a partition <200GB in order to boot the machine. If you are just using the OS 9 System Folder for Classic emulation under OS X, then the partition size does not matter.
you could install one new drive on the PCI card, format it and copy files over from the original drive on the existing ATA channel. Once your backup is fully functional, then you can connect the old drive to the new PCI card. For better performance you should put both drives as their own Master on separate cables into the two ports of the new ATA PCI card, if you can get the cables to fit in there. When copying from one drive to another drive on the same cable, you may have a bottleneck over the shared ATA channel.