Really erasing second hard drive

My Mac Pro won't recognize a second hard drive as a second hard drive. Mac insists on seeing both drives (startup and secondary) as one volume, and then won't list the drives as WD drives in Finder. They are listed in Disk Utility as WD 6400 and WD 5000, correctly. But I want them separated--so that, for instance, Time Machine doesn't object when I try to back-up on the second drive, informing me I'm about to back up on the same volume as the system.
I've tried erasing in Disk Utility, but can't erase without also formatting--either HFS or FAT 32. That is, I can't seem to be rid of the disk. I need a disk that's clean, like new, so the computer will see it that way.
Thanks very much for any suggestion(s),

Well, actually I found what I needed really to erase the drive. Zeroing out in MAC didn't work as even doing that leaves the drive formatted as HFS or FAT. As I noted, there is no choice in Disk Utility. (It took 1 hour, 15 minutes.) It is possible to erase all formatting.
I found a utility at Western Digital that allows for what's called "low-level" formatting, which really erases all formatting. I was able to use the utility in my Bootcamped Windows. When I looked at it afterward in Snow Leopard, Disk Utility showed a disk blanked out--no formatting of any kind, exactly as when shipped from WD. Even though both Mac and Windows recognized the drive and were able to initialize the disk. Disk Utility "saw" the drive regardless of no formatting type. Which was correct. Windows displayed the disk as "unallocated," also correctly. (I couldn't find a way in Windows either to do what I wanted. All that seems to be offered is "Delete Partition," which was useless.)
So I got done what I wanted to do. Alas, that did not help, not even after doing a fresh reinstall of Snow Leopard. I then repartitioned--into four--the disk, using HFS Extended for two and MS-DOS FAT for two. Happily, one can do this in Mac's Disk Utility, since this cannot be done in Windows Disk Manager, which mostly doesn't recognize HFS at all, let alone format a disk with it. But Disk Manager does allow easy conversion of FAT to NTFS, which is what I did with the two partitions formatted FAT in Disk Utility.
These procedures all went smoothly enough, no problems. Two partitions for Time Machine and other Mac files, two for Windows Back-up and other Windows files. Perfect, except that Mac, except in Disk Utility, keeps reporting that two hard drives as one "volume," apparently not unlike in a RAID configuration, so I was told. (I don't have a RAID card nor want one.)
I can still do a Time Machine back-up but don't know what might happen should I ever have to restore from one. It's just very odd that Snow Leopard doesn't recognize two separate hard drives installed in two different bays, though it does in Disk Utility. Very strange!

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