How to set Home Offsets and Manual Home definitions in Marlin correctly?
Normally you wouldn't use the MANUAL_xyz_HOME_POS at all.
Home your machine.
Use a caliper or ruler to measure the distance between the nozzle and the edges of the print bed in both the X and Y direction.
If the nozzle was off the bed in both directions, input these measurements as negative X_MIN_POS and Y_MIN_POS values.
If it was over the bed in either of those directions, you'll need to input them as positive positions.
That should result in your nozzle to be exactly on the edge of the bed after a
G28 X Y
G1 X0 Y0

movement.