It was in the help file after all. I missed it the first time.
I see you found the information. For others benefit this can be found in the ACQUITY Console under the Sample Manager FTN Maintenance pull down menu the choose Calibrate Z Axis. You will need to remove the well plate and using the Z buttons slowly bring the needle down very close to touching the tray bottom, then press Save.
Same as with the regular Acquity, thanks