Ang, it's pretty simple. Maita Heatter explains it in her "bullseye cheesecake" recipe
You simply ladle spoonfuls of alternating batter.
Start with a ladle of dark batter, then carefully pour a light batter directly in the center of that, then another ladleful of dark batter directly in the center of that, etc, etc, etc. The batters push and spread out in concentric circles.
However, since a single bite takes a fair chunk out of a cupcake, you might not get the same "wow" effect as with a big slice of cake.
Try it with those little boxes of Jiffy cake batter.