We report a quantum key distribution using subcarrier wave encoding in Plug&Play configuration. Our detailed study shows how subcarrier encoding operates in a presence of Rayleigh back-scattering, chromatic dispersion and other experimental negative factors that occur in Plug&Play configuration. We propose and experimentally demonstrate a novel regime for the subcarrier wave encoding, where simultaneous detection of two logical states in a single basis is combined with robustness and simplicity of the original protocol. This deep modulation regime shows reliable quantum communication with losses up to 20 dB and promises a twice increase in secret key generation rate in comparison with the original subcarrier wave quantum key distribution in one-way or Plug&Play configurations.