The normal modes and the melting character of a bilayer system consisting of binary charged particles with different charge and/or different mass, interacting through a Coulomb potential and confined in a parabolic trap are investigated. The normal mode spectrum is discussed as a function of the charge ratio (CR) and mass ratio (MR) of the two kinds of charged particles as well as the interlayer separation. We show that the dependence of the normal modes on the excited states can be tuned by varying the CR, the MR, and the interlayer distance. Once the interlayer distance is larger than a critical value, the first excited state corresponds only to the intershell rotation mode. In addition, the intershell rotation melting temperature is discussed as a function of the CR and MR as well as the interlayer separation.