I am brand new to this subject, so this will probably be a very stupid question, but I would appreciate any patient explanations.
S-duality is typically described as a relationship between two QFTs (I am ignoring string theory here) where one theory describing objects interacting with some characteristic strength or coupling constant $g$ is equivalent to a different theory containing different objects (which might be solitonic objects in the dual description, like monopoles) with characteristic interaction strength $1/g$. We can then use the $g \to 0$ limit in one theory to infer information about the strong-coupling dynamics of the dual.
However, according to the renormalization group ideas, any garden-variety QFT will undergo dimensional transmutation and the perturbation theory really ends up being in an effective coupling $g(\mu)$ which flows according to the RG. Even the most simplistic loop calculations in dimensional regularization reflect this, and from a more highbrow point of view, the theory is defined by its UV fixed point. From this point of view, when we look at asymptotically free theories like QCD or gauge theories, the correct question to ask is not "What happens when $g \to \infty$?" but "What does the theory flow to in the infrared?". While it is evident that the IR theory will have some kind of strong-coupling dynamics, how does S duality incorporate this idea?
I know that some examples like Seiberg duality are phrased in terms of the infrared behavior according to the RG, but it seems that the general paradigm is still weak/strong coupling. But even then, exactly what coupling are we referring to? In the classical theory there is just "the coupling", but as soon as you go to the quantum theory dimensional transmutation destroys this, right? Any help would be appreciated.