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.
<?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()
*/
?>
<div class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
<div class="content"<?php print $content_attributes; ?>>
<?php
print render($content);
?>
</div>
</div>
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.
<?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()
*/
?>
<div class="<?php print $classes; ?> clearfix"<?php print $attributes; ?>>
<div class="content"<?php print $content_attributes; ?>>
<?php
// Hide field collection field.
hide($content['field_image']);
print render($content);
?>
</div>
</div>
<section class="row">
<div class=" large-4 columns">
<!-- Render field_image field collection field-->
<?php print render($content['field_image']); ?>
</div>
</section>
Hopefully all of this helps, if not let me know and I can adjust to what exactly you are needing or explain more :)