CC Magic is a program that organizes and manages your CC. I shouldn't mess up your game. I guess it might mess up your CC if you don't use it right. I don't think it would have much impact on game performance.
If I understand correctly, CC Magic is a way to merge CC. Merging .package based CC can help launch times a little bit. I use S3PE to merge my .package based CC instead.
Here's a tutorial on using CC Magic. I've read it a few times but it was too complicated for me. :p