We utilize seismograms recorded by dense linear and 2D arrays across the Banning Fault (BF) and Mission Creek Fault (MCF) strands of the Southern San Andreas Fault (SoSAF) in the Coachella to conduct a comparative analyses of seismic signals and fault structures in the study area. Continuous seismic waveforms are segmented and categorized into earthquake signals, traffic events and non-traffic noise. The seismic signal characteristics reveal differences in the dominant wave types present at the two faults. Beamforming is performed on various signals within 2D subarrays around the fault traces, retrieving apparent Rayleigh wave velocities in the frequency range of 5-10 Hz and various local propagation directions of earthquake phases from regional events. The results indicate prominent bimaterial interfaces in the structures of the BF and MCF, and shallow asymmetric damage zones across both faults with reduced seismic velocities to the northeast in the top ~100 m of the crust. These asymmetric damage zones produce local reversals of the velocity contrast with respect to the structure at depth of several kilometers, and are consistent with preferred propagation directions of earthquake ruptures on both faults to the northwest. The MCF has a more pronounced damaged fault zone, as suggested by scattered seismic wavefields and a larger reduction in subsurface velocities (35.9%) compared to the BF (13.7%). Our observations suggest that MCF is the primary strand of the SoSAF in the area, in agreement with previous studies, and the northeast branch of the BF likely connects to the main BF at depth.