1. Is there any way to run chkdsk on the drive while it is still in the DMS cartridge? I tried from a command window but could not get any results.
You should be able to run chkdsk from a command shell (start, run, cmd, OK). You chkdsk a 'drive' in the sense of a drive partition as opposed to an entire disk.
Take a look here for detailed information on how to do this.
http://support.microsoft.com/kb/315265You'll notice from Windows explorer you have a PHTSYS and PHTDTA drive, you need to check both of these.
2. Can I prep a new drive before I put it in the cartridge? If so, how? I got that impression from your reply.
If you pop the new disk in a USB caddy, then the DMS tools will still allow you to prep. that drive as it it were attached via a cradle. Rather than showing up in the DMS device list as (DMS Cartridge) it will show up as a USB disk, and will only be listed when the tools are running in 'DMS Tools Mode'.