I was wondering how Wordpress remembers the position of metaboxes: session basis, user basis, computer basis? Does it set a cookie? Is it saved in the database?
WordPress saves them in the databas in wp_usermeta as serilized array. For the dashboard all are registered in meta-box-order_dashboard if the meta-box(s) are in metaboxhidden_dashboard they will not be shown. The order will be as saved in database and if not in metaboxhidden_dashboard.
Example the dashboard:
Array ( [normal] => dashboard_right_now,dashboard_recent_comments,dashboard_incoming_links,dashboard_plugins [side] => dashboard_quick_press,dashboard_recent_drafts,dashboard_primary,dashboard_secondary [column3] => [column4] => )
There are also these meta_key(s):