I have mine on a refractor with a rack and pinion focuser so it wont slip like a Crayford would so it is similar to the SCT focuser. I made sure that "IN" on the focus motor was "IN" for focuser movement, set the focuser physically at approx 2mm from fully racked in and set that point as zero on the focus motor, then set the maximum step count to a figure which stops the motor approx 10mm before the focuser is fully racked out (I don't need to go anywhere near that far out to get focus) That way the focus motor will stop in either direction before the physical stop of the focuser itself.
If I put one on my SCT I would do something similar, work out which direction is "IN" on the focus motor then run the focus knob right to that end of its travel and then come back a couple of turns before attaching and zeroing the EAF. Then work out how many steps gets to the other end of the physical focuser travel and set the maximum steps to keep it a couple of turns away from that point, so the focus motor will never drive the mirror to one of the hard stops.
The Celestron focus motor does that as part of its setup routine, it finds the two ends and sets it's internal limits to suit and you should only need to redo that if you do something that moves the focuser without moving the focus motor.
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