This study presents methods to handle deep learning regressions with input and output sequences of different lengths. We discuss the Autoregressive one-step prediction framework and introduce an innovative one-time multi-step (OTMS) prediction approach, based on a custom loss function, that predicts all future steps in a single shot. The presented methodologies are then applied to simultaneously predict the State of Health (SoH) trajectory and estimate the Remaining Useful Life (RUL) of lithium-ion battery cells. Accurate estimates of SoH trajectory and RUL are essential for Battery Management Systems (BMSs), electronic systems that guarantee safety while maximizing performance and extending battery lifespan. In this context, the studied methodologies were compared using a rigorous cross-validation approach. The OTMS model showed better predictions in early cycles, while the Autoregressive model performed better in later cycles, suggesting a hybrid approach between these two methodologies as an optimal solution.