They are talking about not using mysql-query directly but using a class handling all your database stuff.
short (and not working) example that should show you the right way:
class my_db_layer {
var $queries_executed = 0;
function query($sql) {
$this->queries_executed++;
return mysql_query($sql);
}
}
$my_db_object = new my_db_layer();
$r1 = $my_db_object->query('SELECT * FROM users');
echo $my_db_object->queries_executed.'<br />';
$r2 = $my_db_object->query('INSERT INTO visits (visit_time, page_id) VALUES (NOW(), 5)');
echo $my_db_object->queries_executed.'<br />';