Am I suppose to be able to see the other hard drive with linux on it, even though they aren't the same type of file system?
I think you can see it as a drive, but Windows can't access Linux's filesystem. (Not "made in Redmond")

Could I defrag the linux paritition in windows?
Absolutely not! And you'll never need to. Except in truly bizzare circumstances, Linux doesn't fragment (and it has it's own tools anyway).