Dear Sara,
In the FAST primary input file, the only difference in the specifications of an upwind or downwind rotor are in the signs of the OverHang, ShftTilt, PreCone, and ShftGagL inputs (and perhaps HubCM). All but ShftGagL should be negative for an upwind rotor; reversed for a downwind rotor. All coordinate systems, as well as the azimuth angle and pitch angle remain the same between upwind and downwind systems (e.g, the x-axis always points nominally downwind regardless of whether the rotor is upwind or downwind of the tower). See Figures 14 and 16 from the FAST User’s Guide for more information.
I hope that helps.
Best regards,