The nanoscale organization of some classes of ionic liquids is responsible for their singular properties. In this paper, we use polarizable molecular dynamics simulations and small-angle X-ray scattering to probe the structure of two piperidinium- and (trifluoromethylsulfonyl)imide-based ionic liquids ([EBPip$^+$][NTf$_2^–$] and [EOPip$^+$][NTf$_2^–$]) that differ in the alkyl chain length of their cation. The X-ray scattering intensities calculated numerically, from the radial distribution functions, are in excellent agreement with the experimental data. The analysis of the different contributions of the X-ray scattering data allowed us to highlight the correlations responsible for the low q peak observed for the long-chain alkyl cations. New angular analyses showed that anions were more likely to align with alkyl chains as their size increased, inducing angular correlation between anions at larger distances. They also showed that the long alkyl chains of the cations aligned more with each other than the short ones. These more aligned alkyl chains induce a smaller volume of the apolar microdomains compared to the well-studied imidazolium-based ionic liquids, leading to the smaller correlation distance for piperidinium-based ionic liquids.