Can I make one application that covers all car parks?

No, a separate application will have to be made for each of the Zones. You can apply for permits for all six (eight car parks) of the Zones.

Datchet: Horton Road Zone 62402.
Eton: Meadow Lane Zone 62403.
Maidenhead: Grove Road and West Street Zone 62400. Hines Meadow Zone 62404.
Windsor: Alexandra Gardens and Alma Road Zone 62401. Victoria Street Multi-storey Zone 62405.