I saw that SuperUser is using part of my profile from StackOverFlow, but the reputation points haven't migrated across. Is there a simple manner to perform this or do they need to be earned again?
Trust on Stack Overflow dosen't automatically translate to trust on Super User. You'll need to earn reputation here the same way you would on Stack Overflow.
If you get 200 reputation on SO or any other site - all other accounts get an "association bonus" reflecting that you get the platform, and that you can be trusted on other sites to do things like chat and comment.
The benefit of associating accounts is you can use the same login across any site on the network you have an account on.