We present a detailed experimental and modeling investigation of poly(ethylene-4,4＇-biphenyl dicarboxylate) (PEBB) and the related random copolymers poly(ethylene-4,4＇-biphenyldicarboxylate-co-2,6-naphthalene dicarboxylate) (PEBB/EN). We find that different polymorphs exist for the PEBB homopolymer and suggest a second crystal unit cell, different from that which is discussed in the Literature. PEBB/EN copolymers, which are shown here to be random copolymers, are found to be semicrystalline for all naphthanoate concentrations. By combination of DSC, X-ray, and solid-state NMR experiments, uniform comonomer inclusion is proposed for copolymers containing a high amount of EN; for low EN concentrations, these comonomers are rejected from the crystals. By comparison of the comonomer inclusion Gibbs energy, which was estimated from experiments, to those obtained from thermodynamic integration calculations, it was found that PEBB/EN copolymers are able to cocrystallize by aggregation of like and by segregation of unlike repeat units. Once these comonomer inclusions have reached a considerable size, the average defect Gibbs energy reduces to the thermal energy.