It shouldn't be all that complicated at all, and no more so than any other go-to system. Any mount needs to know where it is before it knows where it should go - even the skywatchers own system requires alignment of the mount with where the controller thinks it is.
EQMOD assumes that it is in a predefined position when it connects (DEC = 90*, RA = 6 o'clock), and so if the mount is not pointing in that direction any subsequent go-to movements you make will result in the mount ending up in the wrong place because it has started moving from a different place than where EQMOD thinks it should be moving from.
The initial alignment step can be done either using
this guide from EQMOD about how to set the correct start position, or be done in what I think is a more simple way by manually pointing the scope after the first slew.
If you read the linked PDF, it explains how to set the correct home position - in this case the first go-to should move to the correct place because you have ensured beforehand that both EQMOD and the mount are pointing at the same place. Alternatively instead of setting the home position, you can make a go-to movement to somewhere near the ecliptic, then manually point the scope at the right place (without moving the motors) which ensures that now both EQMOD and the mount are pointing at the same place.
Once the initial alignment is done, each subsequent go-to should go to roughly the right place (the better your polar alignment, the better the accuracy).
Later you can improve the accuracy by doing 3-star alignment which allows EQMOD to correct for any imperfection in the polar alignment and imperfections in the shape of the mount.
---
Now in terms of the AstroEQ, the only part of this which differs from an off-the-shelf Go-To mount, is that AstroEQ needs to know enough about the mount to work out how to map EQMOD commands to physical movements. There are two bits of information the AstroEQ needs to know.
- The gear ratios and motor step size of the mount.
- Which direction the motors rotate in.
The first of those is contained within the configuration file that you have programmed - and this setup is 100% correct for your mount because the tracking speed is exactly correct. If the gear ratios were wrong then the motor would be rotating at the wrong speed when you start sidereal tracking.
The second part should also be within the configuration file.
However not all of the DA kits are the same! Some are wired such that the motor rotates one way when driven "forward", others go in the opposite direction. The major cause of the go-to movements going in completely the wrong direction is that the AstroEQ thinks it is driving the motor clockwise, but in actual fact the motor is spinning anticlockwise - the mount moves the correct distance, but the wrong direction.
In the config utility, there is a button for each axis labelled "Reverse Axis Direction". If you find the mount is moving in the wrong direction, you can click on this button to inform the AstroEQ that it needs to spin the mount the other way. You can test whether you need to enable this option quite easily.
For RA: Start with the setting "off", and test the mount using your skychart software. Slew the mount with the West or East button in EQMOD. Does the telescope move in the same direction as in the sky chart software? If yes, your setting for RA is fine. If no, you need to change the setting to be "on".
For DEC:Repeat the same process as you did for RA, only this time try slewing with the North or South button in EQMOD.Does the telescope move in the same direction as in the sky chart software? If yes, your setting for RA is fine. If no, you need to change the setting to be "on".
Hopefully that makes things a bit clearer.