A little more contextbackground would be useful please?
A copy of the Sailwave file would be useful to better understand how you currently have the file set-up.
If they really are two separate Fleets not what should be called Flights, then I think you need the second of the two scoring options when scoring the series. Also if you do this you will not need any scoring exceptions by Fleet.
I look forward to helping you achieve the results you expect.
Kind regards,
Huw