Create an FPP in an install hook

mymoule.install.php

<?php

/**
 * Creates an FPP.
 */
function mymodule_update_7001() {
  $values = array(
    'title' => 'Title seen in front end',
    'admin_title' => 'Title seen in back end',
    // Make this the machine name of the FPP type.
    'bundle' => 'mypane_type',
    // Make your own UUID with uuidgen on cli or use
    // the value from your exported page-manager page.
    'uuid' => '5495A31E-F3E2-4FB4-9642-03FB62368951',
    // Add fields as required.
    'field_pane_body' => array(
      LANGUAGE_NONE => array(
        array(
          'value' => '<p>This is a rich-text field</p>',
          'format' => 'filtered_html',
        ),
      ),
    ),
  );
  $fpp = entity_create('fieldable_panels_pane', $values);
  entity_save('fieldable_panels_pane', $fpp);
}