The liquid structure of three common ionic liquids (ILs) was investigated by neutron scattering for the first time. The ILs were based on the bis(trifluoromethanesulfonyl)imide anion, abbreviated in the literature as [NTf2]- or [TFSI]-, and on the following cations: 1-ethyl-3-methylimidazolium, [C2mim]+; 1-decyl-3-methylimidazolium, [C10mim]+; and trihexyl(tetradecyl)phosphonium, [P666,14]+. Comparative analysis of the three ILs confirmed increased size of nonpolar nanodomains with increasing bulk of alkyl chains. It also sheds light on the cation-anion interactions, providing experimental insight into strength, directionality, and angle of hydrogen bonds between protons on the imidazolium ring, as well as H-C-P protons in [P666,14]+, to oxygen and nitrogen atoms in the [NTf2]-. The new Dissolve data analysis package enabled, for the first time, the analysis of neutron scattering data of ILs with long alkyl chains, in particular, of [P666,14][NTf2]. Results generated with Dissolve were validated by comparing outputs from three different models, starting from three different sets of cation charges, for each of the three ILs, which gave convergent outcomes. Finally, a modified method for the synthesis of perdeuterated [P666,14][NTf2] has been reported, with the aim of reporting a complete set of synthetic and data processing approaches, laying robust foundations that enable the study of the phosphonium ILs family by neutron scattering.