When you have it ticked in the observatory settings (profile manager) - then it will be slaved automatically every time you start a sequence. For now, if you are just doing some testing (not running a sequence) - you will have to tick the box each time you fire SGP up. It is a safety thing really.........not a hardship 
Yes - getting everything running together is always a chore but when you figure out (measure actually) your offsets and watch the dome follow the scope every night....it will be a joy 