In this work we study the behavior of the optical phonon modes in bilayer graphene devices by applying top gate voltage, using Raman scattering. We observe the splitting of the Raman G band as we tune the Fermi level of the sample, which is explained in terms of mixing of the Raman (Eg) and infrared (Eu) phonon modes, due to different doping in the two layers. We theoretically analyze our data in terms of the bilayer graphene phonon self-energy which includes non-homogeneous charge carrier doping between the graphene layers. We show that the comparison between the experiment and theoretical model not only gives information about the total charge concentration in the bilayer graphene device, but also allows to separately quantify the amount of unintentional charge coming from the top and the bottom of the system, and therefore to characterize the interaction of bilayer graphene with its surrounding environment.