2D networks of Si and Ag nanocrystals have been fabricated in the same SiO2 matrix by Ultra-Low-Energy Ion-Beam-Synthesis. Our synthesis scheme differs from a simple sequential ion implantation and its key point is the control of the matrix integrity through an appropriate intermediate thermal annealing. Si nanocrystal layer is synthesised first due to high thermal budget required for nucleation, while the second Ag nanocrystal plane is formed during a subsequent implantation due to the high diffusivity of Ag in silica. The aim of this work is to show how it is possible to overcome the limitation related to ion mixing and implantation damage to obtain double layers of Si-NCs and Ag-NCs with controlled characteristics. For this, we take advantage of annealing under slight oxidizing ambient to control the oxidation of Si-NCs and the Si excess in the matrix. The nanocrystal characteristics and in particular their position and size can be adjusted thanks to a compromise between the implantation energy, the implanted dose for both Si and Ag ions and the intermediate annealing conditions (atmosphere, temperature and duration).