We combine X-ray absorption, electron spin resonance and Raman spectroscopies, X-ray diffraction and photoluminescence (PL) techniques to determine the structure and luminescence mechanisms in Si nanoclusters (Si-ncls) embedded within Si oxides at various intermediate formation stages. The Si-ncls/oxide systems are fabricated by thermally annealing plasma-enhanced chemical vapor deposited Si-rich Si-oxide films. The structural and chemical orders in the amorphous oxide matrix, the Si-ncls amorphous and crystalline volume fractions and sizes, the dangling bond density and PL spectra and decay rates are followed closely as a function of the annealing temperature. The results can be interpreted by a crystalline core/amorphous shell model for the Si-ncls. The important role of the shell, often ignored in the literature, is discussed. As the Si-ncls crystalline cores grow at the expense of thinning amorphous shells, the PL undergoes a transition from a regime dominated by disorder-induced effects to a situation where quantum confinement prevails.