We present a protocol for simultaneous structural characterization of a confined fluid and the confining Substrate, along with the extraction of site-site pair correlation functions of the liquid of interest. This is based on neutron diffraction experiments, exploiting where feasible the isotopic substitution technique, analyzed through numerical coarse graining calculations and atomistic simulations. All of the subtleties of the experimental procedure, the needed ancillary measurements, and the recipe for tailoring the numerical codes to the real experiment and sample are described in the case of water confined in MCM41-S-15. In particular the excluded volume effects and the relevance of liquid-Substrate cross-correlation terms in the neutron cross section are quantitatively discussed. The results obtained for the microscopic structure of water evidence a non-homogeneous distribution of molecules within the pore, with the presence of water-substrate hydrogen bonds, and a strong distortion of the water-water radial distribution functions with respect to those of bulk water extending at least up to three hydration layers.