This work concerns the study of well-balanced Lagrange-projection schemes applied to the two-layer shallow water system. In particular, a formulation of the mathematical model in Lagrangian coordinates is proposed. Based on the acoustic-transport splitting interpretation, we describe an approximate Riemann solver for the acoustic-Lagrangian step. Then, both an explicit and an implicit-explicit method are proposed, where the latter can allow fast simulations in subcritical regimes. Indeed, since the Lagrange-projection splitting entails a decomposition of the (fast) acoustic and (slow) material waves of the model, an implicit approximation of the acoustic equations allows us to neglect the corresponding CFL condition on the time step.