Hey Ben
MachUpX can easily handle flaperons, i.e. assymetrical aileron deflections resulting from 2 independent control inputs. You would just need to mix the controls for the main wing control surfaces with an aileron control and a flap control. The corrections to section properties due to flap deflection come from thin airfoil theory, and so don't model separated flow, which is what spoilers are meant to generate.
We're currently working to integrate nonlinear airfoil section property databases with MachUp, which may allow for modelling of spoilers.
Cory