In this paper, we have studied a two pass amplifier with a single and two-cell stimulated Brillouin scattering (SBS) phase conjugating mirrors. The role of longitudinal mode structure on the energy reflectivity of the SBS process and temporal behavior of the reflected pulse has been investigated experimentally. The results for different mode structures including single, double and multi-mode pump pulse for SBS mirrors with single and two cells are compared to each other. Our results show that the two cell SBS mirror has some new advantages over the single cell configuration when the laser oscillator operates in multi-mode regime. We found higher reflectivity at high entrance energy for backwardly amplified Stokes pulse. The mode beating become considerably smaller and fluctuations of Stokes pulse are smoothed in the SBS amplifier.