Customize HTML for field in field collection
If your template is being recognized you can access the fields and field content through the $content array. Below is the normal field collection item template file that comes with the field_collection module.

&lt;?php

/**
 * @file
 * Default theme implementation for field collection items.
 *
 * Available variables:
 * - $content: An array of comment items. Use render($content) to print them all, or
 *   print a subset such as render($content['field_example']). Use
 *   hide($content['field_example']) to temporarily suppress the printing of a
 *   given element.
 * - $title: The (sanitized) field collection item label.
 * - $url: Direct url of the current entity if specified.
 * - $page: Flag for the full page state.
 * - $classes: String of classes that can be used to style contextually through
 *   CSS. It can be manipulated through the variable $classes_array from
 *   preprocess functions. By default the following classes are available, where
 *   the parts enclosed by {} are replaced by the appropriate values:
 *   - entity-field-collection-item
 *   - field-collection-item-{field_name}
 *
 * Other variables:
 * - $classes_array: Array of html class attribute values. It is flattened
 *   into a string within the variable $classes.
 *
 * @see template_preprocess()
 * @see template_preprocess_entity()
 * @see template_process()
 */
?&gt;
&lt;div class="&lt;?php print $classes; ?&gt; clearfix"&lt;?php print $attributes; ?&gt;&gt;
  &lt;div class="content"&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;?php
      print render($content);
    ?&gt;
  &lt;/div&gt;
&lt;/div&gt;


Using devel you can use dpm($content); and you will see the below setup.



So as you see in field collection item you could use $content['field_field_1'][0]['#markup'] if your field has extra markup (like for instance if it was set to display as a link to from entity_reference). You could use $content['field_field_1']['#items'][0]['safe_value'] to get the safe value of the field (sanitized). If you want to customize the markup around a certain field you can hide the field and the render it somewhere else. See the below code for an example.

&lt;?php

/**
 * @file
 * Default theme implementation for field collection items.
 *
 * Available variables:
 * - $content: An array of comment items. Use render($content) to print them all, or
 *   print a subset such as render($content['field_example']). Use
 *   hide($content['field_example']) to temporarily suppress the printing of a
 *   given element.
 * - $title: The (sanitized) field collection item label.
 * - $url: Direct url of the current entity if specified.
 * - $page: Flag for the full page state.
 * - $classes: String of classes that can be used to style contextually through
 *   CSS. It can be manipulated through the variable $classes_array from
 *   preprocess functions. By default the following classes are available, where
 *   the parts enclosed by {} are replaced by the appropriate values:
 *   - entity-field-collection-item
 *   - field-collection-item-{field_name}
 *
 * Other variables:
 * - $classes_array: Array of html class attribute values. It is flattened
 *   into a string within the variable $classes.
 *
 * @see template_preprocess()
 * @see template_preprocess_entity()
 * @see template_process()
 */
?&gt;
&lt;div class="&lt;?php print $classes; ?&gt; clearfix"&lt;?php print $attributes; ?&gt;&gt;
  &lt;div class="content"&lt;?php print $content_attributes; ?&gt;&gt;
    &lt;?php
      // Hide field collection field.
      hide($content['field_image']);
      print render($content);
    ?&gt;
  &lt;/div&gt;
&lt;/div&gt;
&lt;section class="row"&gt;
  &lt;div class=" large-4 columns"&gt;
    &lt;!-- Render field_image field collection field--&gt;
    &lt;?php print render($content['field_image']); ?&gt;
  &lt;/div&gt;
&lt;/section&gt;


Hopefully all of this helps, if not let me know and I can adjust to what exactly you are needing or explain more :)