Natural resonance theory (NRT) and natural bond orbital (NBO) analysis have been carried out on a simple symmetrical and an unsymmetrical substituted squaraine with a view of understanding the structure of the latter type of squaraines. It is found that there are some fundamental differences in the structure and bonding between these two types of squaraines particularly in the resonance weights and delocalization energies. These differences are expected to reflect in the low energy transitions and charge transfer in these squaraines. To investigate this, the nature of the lowest energy transitions occurring on excitation in unsymmetrical squaraines has been studied using high-level symmetry adapted cluster-configuration interaction method (SAC/SAC-CI) and compared with reported experimental observations. In general the agreement with the experimental data is very good. The transition dipole moment always lies on the pi-backbone and is quite large in magnitude. The ground state dipole moment in some cases does not change in the excited state upon excitation while in some other cases there is a large reduction/enhancement in the magnitude indicative of some charge rearrangement in this direction. Inclusion of the solvent using the IEFPCM model, a slightly better agreement with the experiment is found in some cases. Studies are carried out with a different basis set and it is found that the change in basis set has very little effect on the transition energies. In the case of weak side donor groups attached to the central ring the larger charge transfer to the central acceptor ring in general takes place from the O- atoms of the squarylium moiety while in the case of strong donors the charge transfer from the O- atoms to the central rings drop down. We have not observed any correlation between the charge transfer in the excited state to the central ring from the side donor groups and the lowest energy excitation in the molecules. Reduction of the HOMO-LUMO gap ( an indication of increase of the diradicaloid character) always leads to a bathochromic shift.