Complex sentence: In the section that BART does run in, there are tunnels on two levels for most of the length of the tunnel, the upper level is used by Muni Metro lines and the lower level is used by BART lines.
Split into simpler sentences: In the section that BART does run in, there are tunnels on two levels for most of the length of the tunnel. The upper level is used by Muni Metro lines and the lower level is used by BART lines.