In your data are you assigning the layer for every node such that they also obey the constraints/dependencies given by the link relationships? If that’s the case, it should not be too difficult to override LayeredDigraphLayout.assignLayers to achieve what you want.
However, if you only wanted to manually assign the layer of several nodes but not the rest, the problem gets much more complicated because it might be impossible to meet the constraints of both the link relationships and the given layers for some of the nodes.