render field collection with already defined custom formatter
So it turns out that the field collection 'field' will be treated like a normal field and rendered properly.  You don't need to load the field with entity_load. (We don't need any of the fields in the collection, we just want the entire collection).  And using field_view_field you can choose your custom formatter:

  //get the nid of the node that contains the field collection from any number of methods
  $node = node_load($nid);
  // the custom formatter was already defined using hook_field_formatter_info() and
  // hook_field_formater_view() (see drupal docs)
  $display = array('type' =&gt; 'custom_formatter_name'); 
  //print or 'return' depending if this is a module or a template file
  print drupal_render(field_view_field('node', $node, 'field_name', $display));


The two hurdles for me were (1) finding out that you can add the custom formatter to field_view_field() and (2) that I needed to print out this info (not return) as I was in a template file, not a function of a module (doh!).