Conditional Fields 2.x for Drupal 6

Conditional Fields 2.x supports theming of forms with conditional fields. The method used is the same outlined here: Theme a CCK input form for CCK2 & CCK3:

  print drupal_render($form['field_controlling']);
  print drupal_render($form['field_controlled']);

However, if you render the individual elements of the fields separately (like, say, each checkbox of field_controlled), you will have to wrap the elements in a wrapper div. You can use theme_conditional_fields_wrapper for this. An example with a checkboxes controlled field: