The coupled-mode method based on the direct global matrix (DGMCM) approach for sound propagation in range-dependent waveguides [Luo et al., "A numerically stable coupled-mode formulation for acoustic propagation in range-dependent waveguides," Sci. China-Phys. Mech. Astron. 55, 572 (2012)] is further developed. The normal mode model KRAKEN is adopted to provide local modal solutions and their associated coupling matrices. As a result, the model DGMCM is capable of providing full two-way solutions for the two-dimensional realistic problems characterized by a penetrable bottom and a depth-varying sound speed profile. In addition, the closed-form expressions of coupling matrices for sound propagation in a range-dependent, two-layer waveguide are proposed. The numerical solutions of the coupling matrices by DGMCM agree well with the analytical solutions. Sound propagation in a penetrable wedge is solved by the updated DGMCM model. The numerical results indicate that the updated DGMCM model is numerically stable and accurate, and can provide benchmark solutions for realistic range-dependent problems.