You want to first ask yourself what you mean by "capacitance of a pair of conductors with different charges". Capacitance is actually defined only for a single conductor. It has become common to extend this definition (to the capacitance of a pair of conductors with equal and opposite charges on them) to the popular version of "charge per unit voltage".
For a general system of conductors, one has :

where

is the capacitance of the i'th conductor.
This comes from solving the Poisson Equation with the Green's Function for the system of conductors, and inverting it (since that would give you

)
So really, the capacitance of a conductor is the charge on it when it is maintained at 1 volt, and all the other conductors are grounded.