I was just wondering if the reputation from both my Super User and Stack Overflow accounts should be combined?
On one of them I have 600~ and on the other I have 100.
Are they supposed to be separate?
Yes, they're separate. That's by design.
What Hyppy said is true but just to elaborate further... Just because you are a programming wiz does not mean you are also a Database/cooking/English/Gaming Expert. You have to prove your worth on each of the sites and show that you deserve to have additional privileges. On a related note- if are member of a Stack Exchange site with over 200 rep and you link your account with another stack exchange site they do give you a 100 rep bonus. At least you can then comment, upvote, and do other basic functions on the site.