How do I alter certain module form output
The form elements for fields (or "Field Widgets" as Drupal calls them) are defined using hook_field_widget_form(), e.g.

function hook_field_widget_form(&amp;$form, &amp;$form_state, $field, $instance, $langcode, $items, $delta, $element) {
  $element += array(
    '#type' =&gt; $instance['widget']['type'],
    '#default_value' =&gt; isset($items[$delta]) ? $items[$delta] : '',
  );
  return array('value' =&gt; $element);
}


They use the form API, and don't have associated templates/themes unless one is explicitly set on a contained element.

You can use hook_field_widget_form_alter() to manipulate the elements; the simplest example (from the docs) would add a class to a particular element:

function hook_field_widget_form_alter(&amp;$element, &amp;$form_state, $context) {
  // Add a css class to widget form elements for all fields of type mytype.
  if ($context['field']['type'] == 'mytype') {
    // Be sure not to overwrite existing attributes.
    $element['#attributes']['class'][] = 'myclass';
  }
}


But obviously you're only limited by what the form API can do. So if you wanted to provide a specific theme for an element:

function MYMODULE_field_widget_form_alter(&amp;$element, &amp;$form_state, $context) {
  if ($context['field']['type'] == 'mytype') {
    $element['#theme'] = 'MYMODULE_some_theme';
  }
}


Then it would just be a matter of implementing hook_theme() and creating the template file to do what you need.

Just for posterity (and because I accidentally answered the question with this first time round); the following relates to formatting the output of a field when its parent entity is displayed:

As listed in Drupal 7 Template (Theme Hook) Suggestions, and originally defined in template_preprocess_field(), these are the built-in patterns you can use to override specific field templates:


field--field-name--content-type.tpl.php
field--content-type.tpl.php
field--field-name.tpl.php
field--field-type.tpl.php


You could also add your own using a template preprocess hook:

function MYTHEME_preprocess_field(&amp;$vars) {
  // This will let you use field--foo.tpl.php as the template name for any fields that pass the condition.
  if (some_condition()) {
    $vars['theme_hook_suggestions'][] = 'field__foo';
  }
}


As far as changing the order of field output goes, that's usually done through the UI in the "Manage Display" forms available for the various view modes for each entity type.