The aim of this study is to increase the capacity of the 1090 MHz secondary surveillance radar (SSR) channel by novel transmission and decoding techniques. In particular, multilateration stations have omni-directional antennae; hence considering aircraft traffic and including the extension of surveillance to cooperating vehicles, the reception of superimposed signals is more and more probable. We propose mitigating this problem by combining frequency agility and source separation techniques; we analyze the pertaining channel capacity improvement, and then evaluate the detection and timing estimation for frequency-shifted and separated signals.