Solution to migrate a field collection
I think you're on the right track. If I'm understanding your question, you won't need to add an extra class.  Instead, you'll want to use your existing Migration class's complete() method, which is called after the node has been created.  Within complete(), you can then use entity_create to create your field collection and entity_metadata_wrapper around your newly migrated node to set a reference to your field collection entity.

In psuedocode,

public function complete($entity, stdClass $row) {
  fc_entity = entity_create(...) 
  $ewrapper = entity_metadata_wrapper('node', $entity);
  $ewrapper-&gt;fc_ref_field-&gt;set( $fc_entity-&gt;nid );
  $ewrapper-&gt;save();
}   


Or something thereabouts. When in doubt, "whatever works" is the correct standard for migration code. Hope that helps get you started!