That would be my advice, get the data off the drive b4 you mess with it. Then have at it. http://www.partitionwizard.com/parti...otable-cd.html
Can`t you put all the data that`s on it now into your my documents folder ? I`m assuming you have data on it, you don`t say. Never seen a dirty drive message.
Make and use the PW Boot CD to delete and format the external.
If you unplug your hard drive when you do your new install, then just plug it back in when your done, all your files will still be on your hard drive. So don`t worry to much. Just have your new ssd drive plugged into port 1 on the mboard.