We present a novel approach to study continuous-wave mode-locking in a waveguide laser in the presence of a gain profile with complex features. We introduce a new simulation approach where we separate the role of gain, nonlinearity, dispersion and saturable absorption elements to provide a better understanding of the interplay between these elements. In particular, we use the simulation to explain synchronised dual-wavelength mode-locking. The results show that despite the existence of dispersion which tends to form separate pulse trains in the laser cavity, the saturable absorber plays a critical role in keeping the different wavelength components synchronised. This work, for the first time, provides insight into existing experimental results. It also demonstrates new methods for studying lasers, especially mode-locking laser, with short laser cavities.