With a partition coefficient how do you decide which solute concentration is the numerator?
The proper way to express the partition coefficient of compound X distributed between an aqueous and organic phase, for example, is:    

$$\mathrm{(K_P)_X = \frac{[X](org)}{[X](aq)}}$$ 

This unambiguously expresses the mathematical fraction to be used in calculating the partition constant for a solute, X between two solvents, aq and org.