After decades of research on the liquid-liquid phase separation (LLPS) of molecules in metallurgy and polymer science, new questions related to this topic keep emerging in both biology and materials science. I will present recent successes of modelling that enabled the interpretation of LLPS morphologies in ultra-white beetle scales and inside living E. coli bacteria, as well as in solvent-cast organic solar cells. Using these examples, I will emphasise the challenges imposed by the presence of many different types of molecules, confinements, and gradual variations in the concentration or in the temperature. For the latter example, I will show how widely used continuum models break down due to strong thermal fluctuations near the critical point. This implies that under these conditions a deep understanding of early-stage morphology formation fundamentally requires modelling at the coarse-grained molecular level. The development of appropriate simulation approaches is expected to be pivotal to the understanding of the interplay between LLPS and molecular self-assembly. This interplay is closely related to long-standing open questions on both the protein aggregation in coacervate precursors relevant to neuropathies, and to the aggregation of polymers in organic solar cells.