Scalability and performance of current flash memories can be improved substantially by novel devices based on Multi-Dot Floating Gate MOSFETs. The multi-dot layer in the very thin gate oxide can be fabricated CMOS-compatibly by ion beam synthesis (IBS). Here, we present both experimental and theoretical studies on IBS of multi-dot layers consisting of Si nanocrystals (NCs). The NCs are produced by ultra low energy Si+ ion implantation, which causes a high Si supersaturation in the shallow implantation region. During post-implantation annealing, this supersaturation leads to phase separation of the excess Si from the SiO2. Till now, the study of this phase separation suffered from the weak z contrast between Si and SiO2 phases in Transmission Electron Microscopy (TEM). Here, this imaging problem is solved by Energy Filtered Scanning Transmission Electron Microscopy (EFSTEM). Additionally, kinetic lattice Monte Carlo simulations of Si phase separation have been performed and compared with EFSTEM images. It has been predicted theoretically that the morphology of the multi-dot Si floating gate changes with increasing ion fluence from isolated, spherical NCs to percolated spinodal Si pattern. These patterns agree remarkably with EFSTEM images. However, the predicted fluence for spinodal pattern is lower than the experimental one. Because oxidants of the ambient atmosphere penetrate into the as-implanted SiO2, a substantial fraction of the implanted Si is lost due to oxidation.