That depends on what you want. If you want the extruder always to stop over the bed you just adjust
// When you have several endstops in one circuit you need to disable it after homing by moving a
// small amount back. This is also the case with H-belt systems.
#define ENDSTOP_X_BACK_ON_HOME 5.0
#define ENDSTOP_Y_BACK_ON_HOME 5.0
so it moves extra mm after hitting endstop and assumes this as xmin/ymin 0 normally.
The other solution is to change xmin/ymin
// Coordinates for the minimum axis. Can also be negative if you want to have the bed start at 0 and the printer can go to the left side
// of the bed. Maximum coordinate is given by adding the above X_MAX_LENGTH values.
#define X_MIN_POS 0
#define Y_MIN_POS 0
If these are negative it means 0 is more to the right and you can tell host/slicer that bed starts at 0 but you can move into negative coordinates as well.
