The consistent frame of reference is that of the direction of the aerofoil through the air. Nick referred to it earlier as the free stream direction. This is generally used as it is the one real constant, whether on an aircraft or in the wind tunnel.
Other frames of reference can be used and in a fixed wing are usually closely mechanically coupled to the above. The fun thing about designing helicopters is that these many frames of reference often change dynamically with respect to each other.
Apply the equations concerned to the aerofoil, and then translate them anywhich way you want. Afterall it's the aerofoil that flies, everything else just hitches a ride.