I am not familiar with either EQMod or the Atlas but there is a box in PhD for “aux mount”. I suspect you could set SGP to control your mount via the driver and then select that driver under aux mount in PhD. Then the guide camera you are using and “on camera” for the other two boxes. “On camera” uses the ST4 and guide cable to guide direct from the guide camera and the “aux mount” gives PhD the needed information coming from your mount.
Really a PhD question, actually.