Simon,
If you set up a start time in your sequence, it will automatically unpark the mount. If you tell it to 'slew' in the sequence, it will automatically slew to the first target. And, if you turn on 'center' in the sequence, it will also center the target.
PHD2 has options for calibration and saving calibrations. SGP would prefer that you have it calibrated already when you start, but you can force PHD2 to re-calibrate per target or have it re-use calibration (if you have an obs for instance).
Hope that helps,
Chris