Making multi-column checkboxes/radios with theming is not possible. Drupal expands checkboxes/radios into a set of chrildren checkbox/radio form element inside. You need to control all the children checkbox inside but if you do it with theming the checkboxes, by the time you get to theme it, it's too late. All the children checkbox are already rendered.
See my multi-column checkboxes radios module
http://drupal.org/project/multicolumncheckboxesradios
Making multi-column checkboxes/radios with theming is not possible. Drupal expands checkboxes/radios into a set of chrildren checkbox/radio form element inside. You need to control all the children checkbox inside but if you do it with theming the checkboxes, by the time you get to theme it, it's too late. All the children checkbox are already rendered.
My module does it in a different way.