We investigate the effect of periodic driving by an external field on systems with attractive pairing interactions. These include spin systems (like the ferromagnetic XXZ model) as well as ultracold fermionic atoms described by the attractive Hubbard model. We show that a well-known phenomenon seen in periodically driven systems--the renormalization of the exchange coupling strength--acts selectively on bound-pairs of spins/atoms, relative to magnon/bare atom states. Thus one can control the direction and speed of transport of bound-pair relative to magnon/unpaired atom states, and thus coherently achieve spatial separation of these components. Applications to recent experiments on transport with fermionic atoms in optical lattices which consist of mixtures of bound-pairs and bare atoms are discussed.