Liposomal systems are advanced carriers of active substances which, thanks to their ability to encapsulate these substances, significantly improve their pharmacokinetics, bioavailability, and selectivity. This article presents the results of spectroscopic studies for a selected compound from the 1,3,4-thiadiazole group, namely 4-[5-(naphthalen-1-ylmethyl)-1,3,4-thiadiazol-2-yl]benzene-1,3-diol (NTBD, see below in the text), in selected liposomal systems formed from the phospholipid 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC). Detailed spectroscopic analyses were carried out using electronic absorption and fluorescence spectroscopy; resonance light scattering (RLS) spectra measurements; dynamic light scattering (DLS); as well as time-resolved methods—fluorescence lifetime measurements using the TCSPC technique. Subsequently, based on the interpretation of spectra obtained by FTIR infrared spectroscopy, the preliminary molecular organization of the above-mentioned compounds within lipid multilayers was determined. It was found that NTBD preferentially occupies the region of polar lipid headgroups in the lipid multilayer, although it also noticeably interacts with the hydrocarbon chains of the lipids. Furthermore, X-ray diffraction (XRD) techniques were used to study the effect of NTBD on the molecular organization of DPPC lipid multilayers. Monomeric structures and aggregated forms of the above-mentioned 1,3,4-thiadiazole analogue were characterized using X-ray crystallography. Interesting dual fluorescence effects observed in steady-state fluorescence measurements were linked to the excited-state intramolecular proton transfer (ESIPT) effect (based on our earlier studies), which, in the obtained biophysical systems—liposomal systems with strong hydrophobicity—is greatly enhanced by aggregation-induced emission (AIE) effects. In summary, the research presented in this study, concerning the novel 1,3,4-thiadiazole derivative NTBD, is highly relevant to drug delivery systems, such as various model liposomal systems, as it demonstrates that depending on the concentration of the selected fluorophore, different forms may be present, allowing for appropriate modulation of its biological activity.