load the jquery.min.js at the bottom of the page (also for 6.x vers)

Below code can be used to place the javascript .js file at the bottom of the page:

In template.php file:

<?php
// Used in conjunction with https://gist.github.com/1417914
/**
* Implements hook_preprocess_html().
*/
function THEMENAME_preprocess_html(&$vars) {
$path = drupal_get_path('theme', 'THEMENAME');
drupal_add_js($path . '/js/jquery.min.js', array('scope' => 'footer', 'weight' => -1, 'preprocess' => FALSE));
}
/**
* Implements hook_process_html().
*/
function THEMENAME_process_html(&$vars) {
$vars['foooter'] = drupal_get_js('foooter');
}

This falls outside the scope of what this project should be doing (it's goal is to update jQuery and subsequent jQuery related code, not alter where it all shows up). For something like this, you would be better off using https://www.drupal.org/project/advagg.