No man.
You should format your master drive first, because that is your booting OS.
Once you install the whole things and is happy with it, you can just format your second hard drive via "My Computer" and right click on your D:\, format.
Or you can do this from the Disk management..
Right click on "My Computer" and select Manage...
Go to disk management.
Look for your secondary hard drive. You can right click on it and select format.
Make sure you take your data back before you do this.