How to add a filepath to a file uploaded in form API
Whenever I use a file field in the submit handler I use:

$validators = array('file_validate_extensions' =&gt; array('csv'));
if ($file = file_save_upload('upload', $validators)) {


You can add an optional argument to file_save_upload after $validators which is $destination, take a look at https://api.drupal.org/api/drupal/includes!file.inc/function/file_save_upload/7 for more details