ShyGuy,
The suggestion by Corky might not have struck you for its total usefullness, so I will elaborate a bit . . .
What he was talking about is having a removable HDD tray in one of your front bays. This will allow you to turn the secondary HDD on and off as needed. Once you have a completely loaded and tweaked system, you go to full power OFF, turn the key on the removable HDD and then fire the system back up using Drive Copy 4 (or above) in its bootable floppy form. This boots to its own operating sysyem and doesn't care what format your HDD is in.
Once booted, you have the option (among other things) to make a complete mirror copy of your entire HDD. This, of course, is presuming that you use the same size drive as your primary HDD. You then turn the system off (power OFF), unlock the drive to keep it from being on when you reboot, then reboot the system as normal.
You now have a complete copy of your current configuration and all that would be necessary to get back into operation in case of a failure or corruption on your primary HDD is boot from the DC4 floppy as outlined above and this time copy drive two to drive one. 10 to 20 minutes later, depending on the size and speed of your drives, you are back up and running with a complete OS plus all your programs and settings and data intact.
The obvious entension of this is that you make a fresh copy to your "backup" drive on a regular basis and you have spent far less time with the actual backups . . . they are complete including all data and settings current to that date, plus in case of an actual hardware failure on the primary HDD you can be back in operation in the time it takes to phylically swap your drives.