Hi Craig!
You are correct that all locos must be profiled for you to use them in automatic. (Also, if you want them to auto stop in correct position while using schedules in manual and are auto switched to a passing track or have a stop signal during a train meet.)
When you go to the selected engine's properties, click the Speed tab.
Now click: "Adjust Speed Steps:
The first thing needed is to do a general calibration of the selected engine using three different speeds. This calibration is close and will get you near the markers you have set.
For more accuracy, you now must perform the "Advanced Fine Tuning". This is very tedious and time consuming, but necessary if you want the marker numbers to be accurate. The "marker" numbers you use is in inches and will be near correct after this adjustment.
USE HELP and the MANUAL for these adjustments.
I have a few locos that I used the fine tuning, but most have been profiled using only the first calibration. I then do a hit and miss by adjusting the markers until I am satisfied...doesn't take long
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Keep in mind that your train load, track voltage, and engine performance will affect these settings (Also, acceleration and deceleration settings.). Each engine/train must be adjusted. Many of my markers are custom set for the individual engine/trains to compensate for the these variables