Brain function require the control of inter-circuit interactions on time-scales faster than synaptic changes. In particular, efficiency and direction of influence and communication between neural populations (described by the so-called directed functional connectivity) must be reconfigurable even when the underlying structural connectivity is fixed. Such influences can be quantified through time-series analyses of time-series of neural activity (such as Transfer Entropy). But how can manifold functional networks stem from fixed structures? Considering model systems at different scales, from neuronal cultures to motifs involving few brain areas and up to brain-wide thalamocortical networks, we show that ``function and information follow dynamics'', rather than structure. Different dynamic states of a same structural network, characterized by different synchronization properties, are indeed associated to different directed functional networks, corresponding to alternative information flow patterns (functional multiplicity). At the same time, different structural circuits generating very similar dynamics can give rise to equivalent functional networks (structural degeneracy). Here we show how it is possible, taking into account switching between collective states of the analyzed circuits, to provide a picture of directed functional interactions in agreement with a ``ground-truth'' description at the dynamical systems level. We put then particular emphasis on explaining how multi-stability between attractors in a subcritical dynamical regime might account for empirically observed structured patterns of non-stationarity in resting-state BOLD functional connectivity.