If you use a backup program to backup to the slave drive, the fact that you have the OS on both drives should not be a problem. The backup prog is likely to both compress and rename the files it backs up.
All my backed up files have been. So setuplog.exe became setuplog.exe.nzd.000
If you do a cut and paste this might cause problems. But as you say you have already got a backup util it should not be a problem.