I've taken the liberty to rewrite your query to use table aliases to make it easier to read. I've also rewritten it to use the JOIN operator, since this is how we normally write joins in SQL Server. Furthermore, I've removed brackets not needed, again to improve legibility.
Finally, I have changed the GROUP BY and ORDER BY clause to meet the requirement in your question.
SELECT Count(*) AS TotalNumberFlying, M.MfrMdlCode, F.MFR, F.MODEL
FROM AircraftReg.dbo.MASTER AS M
JOIN AircraftReg.dbo.FixedWingMultiEngine AS F ON M.MfrMdlCode = F.CODE
GROUP BY GROUPING SETS ((M.MfrMdlCode, F.MFR, F.MODEL), ())
ORDER BY grouping(F.MFR), TotalNumberFlying