The Graphical Scheduler is an interactive Gantt chart to display the base NAV/BC schedule and give the user a simple method for changing when or where operations schedule by dragging them in that Gantt chart view. Whereas MxAPS is a completely separate planning and scheduling system that has its own rules for sequencing and grouping. It bypasses many of the limitations of the built in scheduling Business Central has by allowing multiple work centers or machine centers per operation, adding a secondary constraint model to handle tooling and labor resources, and it can consider setup reduction between items that share similar attributes.
As to when to use one over the other I’d say if you are interested in a quick drop in to let users make manual schedule tweaks to what Business Central plans in a Gantt chart view, go with the Graphical Scheduler. If you are looking to add scheduling intelligence to the process to build better constraint based schedules using software and trying to limit the amount of manual intervention that has to take place MxAPS would be what you want.