When you are creating the site, you are given an option to break the security inheritance and potentially create new Owner, Member, and Visitor groups (or at least specify which groups are used for those roles).
If you have already created the sites with inherited permissions, then you can go to SITE ACTIONS > SITE SETTINGS > (MODIFY ALL SITE SETTINGS) > ADVANCED PERMISSIONS. Then choose Actions > Edit Permissions and adjust them manually to specify the new Owner group used.
