There is no way to manually calibrate the endstops on the Kossel Pro. In theory, it should all be handled by the automatic calibration. However in practice this is not always the case. There are some lengthy posts over on the Kossel Pro forums about this issue. I will do my best to give an overview of the solutions here.
Disable the probe and switch to MatterControl's software leveling. This will have you manually measure the height of the bed at various points using paper as a feeler gauge.Use shims to ensure the correct distance between the arm joints. The basic problem is that, due to the geometry of the delta system, if the arms are not perfectly parallel with each other it will cause the end effector to to tilt slightly as it moves from one place to another. This tilting means that the probe can move slightly up or down relative to the nozzle, which throws off the measurements it is taking. To take care of this problem, ZT Automations is now selling a set of shims you can use to ensure that the arm joints are evenly spaced. Upgrade to a better probing system, like Force Sensing Resistors (FSRs). These are much more accurate since they detect the nozzle itself pressing against the bed, instead of a seperate probe. Ultimachine sells a $40 FSR kit with all the electronics you need. You will also need to print some new bed mounts and remove the probe offset in the firmware configuration.