Processing an MPEG elementary stream contained in multiple PID streams in a conditional access overlay environment. A multi-program transport stream contains numerous video and audio elementary streams. Critical packets in the elementary streams are encrypted with two different encryption schemes creating a stream having multiple PID values. The streams are then sent from the headend to individual set-top boxes. One encryption scheme can be decoded by the incumbent set-top box and the second encryption scheme can be decoded by the overlay set-top box. The overlay set-top box uses a dual filter system to filter and decode the PIDs for each video and audio stream of the desired program.