Get All In One SEO Pack to use custom field instead of Content

You can not specify which field, but you can use the filter *aioseop_description* to do whatever you want with the description before presenting. So technically, you can use your custom field as follows (untested) :

add_filter('aioseop_description','my_custom_description');
global $post;
function my_custom_description($text) {
$mycustomseo = get_post_meta($post->ID, 'my_custom_field', true);
return $mycustomseo;
}

Replace *my_custom_field* with your custom field.

Source Ref : http://4coder.info/en/blog/2011/all-in-one-seo-pack-customization/