Context. The GRAVITY+ upgrade implies a complete renewal of its adaptive optics (AO) systems. Its complex design, featuring moving components between the deformable mirrors and the wavefront sensors, requires the monitoring and auto-calibrating of the lateral mis-registrations of the system while in operation. Aims. For preset and target acquisition, large lateral registration errors must be assessed in open loop to bring the system to a state where the AO loop closes. In closed loop, these errors must be monitored and corrected, without impacting the science. Methods. With respect to the first requirement, our method is perturbative, with two-dimensional modes intentionally applied to the system and correlated to a reference interaction matrix. For the second requirement, we applied a non-perturbative approach that searches for specific patterns in temporal correlations in the closed loop telemetry. This signal is produced by the noise propagation through the AO loop. Results. Our methods were validated through simulations and on the GRAVITY+ development bench. The first method robustly estimates the lateral mis-registrations, in a single fit and with a sub-subaperture resolution while in an open loop. The second method is not absolute, but it does successfully bring the system towards a negligible mis-registration error, with a limited turbulence bias. Both methods proved to robustly work on a system still under development and not fully characterised. Conclusions. Tested with Shack-Hartmann wavefront sensors, the proposed methods are versatile and easily adaptable to other AO instruments, such as the pyramid, which stands as a baseline for all future AO systems. The non-perturbative method, not relying on an interaction matrix model and being sparse in the Fourier domain, is particularly suitable to the next generation of AO systems for extremely large telescopes that will present an unprecedented level of complexity and numbers of actuators.