In part 1 of this two-paper series, a local order parameter framework was put forth that could track the changes occurring when block copolymer-like mesophases formed from a disordered state. The framework was developed using a two-particle model and involved identifying the local symmetries and geometric motifs that were unique to a given mesophase. In this paper, this framework is suitably modified to track the mesophase formation of standard coarse-grained bead–spring simulation models of polymers and oligomers. In particular, a mesoscale chain model typically employed with dissipative-particle dynamics is used to study the ordering transition of a linear symmetric diblock copolymer into a lamellar phase, and a more detailed bead–spring model of branched bolaamphiphile molecules is used to track the formation of a single diamond phase. These applications illustrate the robustness of the method in handling molecules with intramolecular degrees of freedom (including multiple chemical blocks and branched ...