@dnube As I am not familiar with Foster Systems I can't be very specific about how to set things up. The only two things I would be confident about: 1) Trying to mesh AstroMC & SGP for controlling the dome is sure to lead to problems. Use either one or the other.....and 2) SGP had a few problems initially but all sorted now. SGP has the ability to control the dome in tandem with the mount once all the numbers are fed in correctly.....and you should be OK for full automation.
Again....not being familiar with AstroMC, I would not be surprised if the E or W exercise is just to give your dome an orientation angle....it will take it from the mount when there are no offsets between how they are pointing. If that gives you an angle in the dome software then that is a 'sync'. I would mark that dome position, note the angle.....then you will always have a reference point to sync your dome on should the need arise to check anytime in the future...........but once done, I would say let SGP take it from there.
I hope someone else is on here with similar dome to you - perhaps they can let you know for sure how they set things up.
As above: I think that is just allowing AstroMC to get an angle from the mount...Hopefully if you do that....you will be able to see that dome angle somewhere in that software.....then do as I suggested....mark the spot, note the angle and you will always have a reference angle to sync the dome to.....even when just using SGP.