Secondary electron injection (SEI) is used for programming NVM cells having separate charge storage areas in an ONO layer, such as NROM cells. Various combinations of low wordline voltage (Vwl), negative substrate voltabe (Vb), and shallow and deep implants facilitate the process. Second bit problems may be controlled, and retention and punchthrough may be improved. Lower SEI programming current may result in relaxed constraints on bitine resistance, number of contacts required, and power supply requirements.