Nonlinear optical Sum and Difference-Frequency spectroscopies are used to probe and model the surface of thiophenol-functionalised gold nanoparticles grafted on a Si(100) substrate through two different silanization procedures. By scanning the [980-1100 cm(-1)] infrared spectral range with the CLIO Free Electron Laser, ring deformation vibrations of adsorbed thiophenol are investigated. Quantitative data analysis addresses three levels of organization: microscopic, nanoscopic and molecular. Grafting with p-aminophenyl-trimethoxysilane shows an increase of around 40% in surface density of nanoparticles (N(s)) as compared to 3-aminopropyl-triethoxysilane. The relative amplitudes of the resonant and nonresonant contributions to the SFG and DFG spectra are discussed in terms of N(s), Fresnel reflectivity factors and local amplification of the nonlinear signals by coupling to the surface plasmon of the particles. They are shown to quantitatively scale with N(s), as measured by atomic force microscopy. Vibration mode assignment is performed through a critical analysis of literature data on IR and Raman spectroscopies coupled to DFT calculations, for which a methodology specific to molecules adsorbed on gold atoms is discussed.