To create template file for form in drupal you can use hook_theme() For Example: Create a custom module i have created a module name custom_profile so hook is replaced by custom_profile

<?php
/**
* Implementation of hook_theme()
*/
function custom_profile_theme() {
  return array(
    'custom_profile_publications' => array(
      'arguments' => array('form' => NULL),
      'template' => 'create-publication',
    ),
  );
}
// Where custom_profile_publications is form id
// arguments form is the argument passes to the tpl file
// create-publication is the tpl file created inside the module tpl file named as create-publication.tpl.php
// user $form and drupal_render() in the template file
?>