Whats the proper way to preprocess field collection items to add first and last class names?
You would normally do this in MYTHEME_preprocess_field_collection_item(), but field collection items don't have their own preprocess. Fortunately, they're entities, so you can use entity preprocess to create your own field collection preprocess function:

/**
 * Implements template_preprocess_entity().
 */
function MYTHEME_preprocess_entity(&amp;$variables, $hook) {
  $function = 'MYTHEME_preprocess_' . $variables['entity_type'];
  if (function_exists($function)) {
    $function($variables, $hook);
  }
}

/**
 * Field Collection-specific implementation of template_preprocess_entity().
 */
function MYTHEME_preprocess_field_collection_item(&amp;$variables) {
  $variables['classes_array'][] = 'your-class-here';
  // Plus whatever other preprocessing you want to do.
}