The Axes should never move when in E-Stop, if they are then it suggests you do not have an Enable signal controlled from Mach/CSMIO.
DAC offset is likely needed when CSMIO is in control and Mach out of E-Stop, to get the correct value you just press the DAC Offset button and it should work it out for you instantly.
Normally for steps per unit you would use the encoder counts per rev and divide by the distance travelled but as you have linear scales you will need to know the resolution of the scales.
If for example each graduation of the scale is 0.005mm then you would have 200 per mm, this however would likely need to be multiplied by 4 for quadrature, so 800 would be the value.
To know the pulses per revolution (encoder count) you would need to know the distance your axes travel for one revolution of the screw and then calculate with the graduations of the scale. if for example it was 10mm then your pulses per revolution would be 8000 (10 x 800)
AutoTuning should start instantly and not take too long, likely your steps per unit being wrong are the problem there.
Hood