field_collection_save.module

<?php
$field_collections = array(); // <--- change to your array of field collection data

// Time to save field_collection_item entities.
foreach ($field_collections as $field_collection_name => $field_collection_entries) {
  foreach ($field_collection_entries as $delta => $field_collection) {
    // Everything should be in place from before. Just save it.
    $field_collection->save(TRUE);
  }
}

node_save($node);