Full nucleation control for deposited functional molecules on pre-patterned surfaces is of major technological relevance. To understand the nucleation behavior we combine the numerical solution for the evolution of the adatom concentration with standard nucleation theory. From the qualitative change in nucleation behavior upon variation of the pattern spacing and coverage we show why the quality of nucleation control can vary significantly in different parameter regimes. In some limits analytical expressions can be formulated for the nucleation control. Our analysis provides a theoretical explanation for previous experimental observations [Wang et al, PRL 98, 225504 (2007)].