This paper puts forth a new, reconfigurable intelligent surface (RIS)-assisted, uplink, user-centric cell-free (UCCF) system managed with the assistance of a digital twin (DT). Specifically, we propose a novel learning framework that maximizes the sum-rate by jointly optimizing the access point and user association (AUA), power control, and RIS beamforming. This problem is challenging and has never been addressed due to its prohibitively large and complex solution space. Our framework decouples the AUA from the power control and RIS beamforming (PCRB) based on the different natures of their variables, hence reducing the solution space. A new position-adaptive binary particle swarm optimization (PABPSO) method is designed for the AUA. Two twin-delayed deep deterministic policy gradient (TD3) models with new and refined state pre-processing layers are developed for the PCRB. Another important aspect is that a DT is leveraged to train the learning framework with its replay of channel estimates stored. The AUA, power control, and RIS beamforming are only tested in the physical environment at the end of selected epochs. Simulations show that using RISs contributes to considerable increases in the sum-rate of UCCF systems, and the DT dramatically reduces overhead with marginal performance loss. The proposed framework is superior to its alternatives in terms of sum-rate and convergence stability.