I just add them in phpMyAdmin. But, I did write a product that I shared with someone and this is the query I used to add a new column to the thread table:
Code:
$db->query("ALTER TABLE " . TABLE_PREFIX . "thread ADD verify_status SMALLINT(5) UNSIGNED DEFAULT '0' NOT NULL");
That was to add a new column of type smallint which is probably what you want. Default is '0' and it's not null.
If you go for this approach of adding a new 'order' column, don't forget you need to modify the /admincp/ranks.php page to include it on your User Rank page in the Admin CP