We analyze the charge dynamics of a superconducting single-electron transistor (SSET) in the regime where charge transport occurs via Cooper-pair resonances. Using an approximate description of the system Hamiltonian, in terms of a series of resonant doublets, we derive a Born-Markov master equation describing the dynamics of the SSET. The average current displays sharp peaks at the Cooper-pair resonances and we find that the charge noise spectrum has a characteristic structure which consists of a series of asymmetric triplets of peaks. The strongest feature in the charge noise spectrum is the triplet of peaks centered at zero frequency which has a peak spacing equal to the level separation within the doublets and is similar to the triplet in the spectrum of a driven, damped, two-level system. We also explore the backaction that the SSET charge noise would have on an oscillator coupled to the island charge, measurement of which provides a way of probing the charge noise spectrum.