the side menu is created in the CSSMenuWriter/intermediate.php file.
you could edit the recordsets herre to add an order by clause
the reocrdsets are at lines 42:
$query_ProductCategories = sprintf("SELECT * FROM categories WHERE CategoryParent = %s", GetSQLValueString($colname_ProductCategories, "int"));
and 69:
$query_ProductMenu = sprintf("SELECT * FROM categories WHERE CategoryParent = %s", GetSQLValueString($catParam_ProductMenu, "int"));
you could edit those to:
$query_ProductCategories = sprintf("SELECT * FROM categories WHERE CategoryParent = %s ORDER BY CategoryName DESC", GetSQLValueString($colname_ProductCategories, "int"));
and 69:
$query_ProductMenu = sprintf("SELECT * FROM categories WHERE CategoryParent = %s ORDER BY CategoryName DESC", GetSQLValueString($catParam_ProductMenu, "int"));
reordering the categories manually is not supported.