Send M500 after calibration. This will save the M665, M666, M307 and G31 parameters in file config-override.g. Then make sure that your config.g file invokes config-override.g at the end, which is done with command M501.
Alternatively, after running auto calibration, send M665 and M666 without parameters to see what values auto calibration has produced. Then edit those values into the M665 and M666 commands in config.g. The endstop corrections go in the XYZ parameters of the M66 command, and the tower angle corrections go in the M665 X and Y parameters.
Large delta printer [miscsolutions.wordpress.com], E3D tool changer, Robotdigg SCARA printer, Crane Quad and Ormerod
Disclosure: I design Duet electronics and work on RepRapFirmware, [duet3d.com].