You've hit upon the fact that a set of physics equations, on its own, doesn't tell you which values should be the "inputs" (coming in from outside the problem you're solving), and which values should be the "outputs" (solved by the equations, given the specific inputs). Physicists usually have a context, along with causal intuitions, which tell them which values should be "inputted". Also, sometimes the choice is one of calculational convenience.
If the context is an experimenter controlling a bunch of charges, wiggling them at will to create chosen currents, then our causal intuition tells us that the full spacetime history of $J^\nu$ should be an input, and the first equation you give can be used to solve for the fields generated in this manner. But consider a different context, where the experimenter is controlling the fields (say, a laser operator), wiggling the fields at will, while merely setting up the initial charges. Now the natural way to use these equations is to input the fields and the initial charge distribution, and then solve for the future charge distribution, using your final equation. The common thread is that the "input" tends to be what we imagine controlling, from outside the modelled system. (This follows the modern "interventionist" view of causation, where the "cause" is where we imagine we are able to intervene from outside the system.)
Remarkably, there's no one right answer here. One could claim that the "right" way to do it is to start with the initial charge and field distribution as an input, but that doesn't work well if you're externally controlling anything at all, manipulating charges and/or fields as time goes on. (Not to mention that self-consistently solving such equations is profoundly difficult!) In practice, how one uses these equations really is context-dependent. You need more than just the bare equations to solve physics problems. Along with the equations, to make them useful, one generally needs a causal model, supplying some knowledge about where the interventions are happening in any given context.