Hey there, MJDRAKE.
What did you try exactly via CMD? Are you sure you are tying to format the secondary storage drive, because there's no reason for you not to be able to delete or format partitions if you haven't booted from that drive?
Basically you can go ahead and try the low level format with DISKPART (via CMD). Here's how to do it:
1. Open CMD (Command Prompt) as administrator.
2. Type
diskpart and press "enter"
3. Type
list disk and press "enter", you'll see all the storage devices connected to your computer and you should be able to recognize the drive you wish to format, by its size.
4. Type
select disk X and press "enter" (where X is the number of the drive you wish to format, so make sure that you've selected the correct one - e.g. if the drive you wish to format is disk 1, type: select disk 1)
5. Type
clean and press "enter", then wait for the process to finish.
After you do this, you'd have to initialize the drive before you are able to create and format new partitions. Here's how to do it:
How to initialize or write a signature to a secondary hard drive or Solid State drive in Windows.
Hope that helps.
Boogieman_WD