We investigate excitation energy transfer occurring from encapsulated dye molecules to s-SWCNTs, which results in luminescent SWCNT excitons. We exploit the high-throughput and chiral selectivity of polyfluorene wrapping methods to generate dispersions of s-SWCNTs with dye encapsulation. We demonstrate that the selectivity of the polyfluorene polymer for semiconducting chiral distributions is not affected by the presence of encapsulated molecules. Tracking the excited state transient absorption signatures of excitation energy transfer provides detailed information regarding dynamics of both the encapsulated dye and s-SWCNTs. We observe sub-picosecond excitation energy transfer of excitons generated in dye molecules to the surrounding s-SWCNTs. Photoluminescence excitation maps reveal that the absorption of encapsulated dye molecules depends sensitively on the diameter of the s-SWCNT in which they are encapsulated. We consider a simple molecular exciton model to describe aggregate formation within the s-SWCNT endohedral volume, which reveals that the dye molecules adopt unique aggregate structures that are defined both by a competition between intermolecular interactions between the dye molecules and confinement effects due to the s-SWCNT diameter. Small molecule encapsulation in s-SWCNTs serves as a strong platform to control intermolecular interactions in small molecule systems through confinement, which opens up the possibility of enhancing photo-induced extraction of energy and charge in s-SWCNTs solar photoconversion systems.