How to change default position of WP meta boxes?

You can remove the default meta boxes with remove_meta_box and re-add them in a different position with add_meta_box:

add_action('do_meta_boxes', 'wpse33063_move_meta_box');

function wpse33063_move_meta_box(){
    remove_meta_box( 'postimagediv', 'post', 'side' );
    add_meta_box('postimagediv', __('Featured Image'), 'post_thumbnail_meta_box', 'post', 'normal', 'high');
}

This will remove it from the side column and add it to the main column. change post in this example to whatever your custom post type is named.