Combining graphene and the insulating hexagonal boron nitride (h-BN) into two-dimensional heterostructures is promising for novel, atomically thin electronic nanodevices. A heteroepitaxial growth, in which these materials are grown on top of each other, will be crucial for their scalable device integration. However, during this so-called van der Waals epitaxy, not only the atomically thin substrate itself must be considered but also the influences from the supporting substrate below it. Here, we report not only a substantial difference between the formation of h-BN on single- (SLG) and on bi-layer epitaxial graphene (BLG) on SiC, but also vice versa, that the van der Waals epitaxy of h-BN at growth temperatures well below 1000 °C affects the varying number of graphene layers differently. Our results clearly demonstrate that the additional graphene layer in BLG enhances the distance to the corrugated, carbon-rich interface of the supporting SiC substrate and thereby diminishes its influence on the van der Waals epitaxy, leading to a homogeneous formation of a smooth, atomically thin heterostructure, which will be required for a scalable device integration of 2D heterostructures.