A mechanistic understanding of internal variability of the climate is crucial as internal variability has a strong influence on regional to local climate projections throughout the 21^st century. The Atlantic Meridional Overturning Circulation (AMOC) strongly impacts regional to local climate and geological evidence suggests (multi-)centennial AMOC variability (mCAV) is a feature of the Mid- to Late Holocene climate. However, our understanding of the spatio-temporal aspects and underlying mechanisms of mCAV is very limited. Understanding the mechanisms behind Holocene mCAV requires a methodology that isolates spatio-temporal patterns of variability and is applicable to both climate model output and the geological archive. Multi-channel singular spectrum analysis (MSSA) has been successfully applied to climate model output to identify and isolate basin-wide spatio-temporal modes of variability. However, it remains unclear if the correct modes can be identified, and if these modes retain their spatio-temporal coherence, when based on input data that is constrained by relatively sparse locations where proxy records are available. Here, we explore this issue in a transient Late Holocene simulation of an earth system model of intermediate complexity that is known to contain mCAV. Our results show that under constrained input data MSSA can be used to identify robust modes of simulated mCAV and that the modes retain their spatio-temporal coherence within at least the northern and eastern North Atlantic. These findings suggest MSSA can be a suitable tool to extract basin-wide modes of variability and associated spatio-temporal patterns from geological reconstructions. This motivates further work that incorporates uncertainties associated with geological reconstructions into the MSSA methodology. Furthermore, our findings motivate the identification and clustering of temperature based phase-relationships in different climate models that contain different mechanisms of mCAV.