In order to understand the effects of disorder and defects in oligomers and polymers on the localization of excitons, we investigated the spectral properties of the squaraine B hexamer using long range corrected tight-binding TDDFT (lc-TDDFTB) and Frenkel-exciton model based calculations. Employing classical molecular dynamics, the cisoid indolenine squaraine hexamers helix was propagated in DCM and acetone to obtain ensembles of realistic structures, which naturally exhibit considerable disorder. The trajectories together with several model squaraine systems were studied to show the profound effects of disorder in the superstructure and disorder of the local monomer geometry on optical properties like absorption and exciton localization. We further compared lc-TDDFTB and exciton theory derived spectral data to related experimental data on absorption, exciton transfer and localization in squaraine polymers and oligomers.