For optimal results in phase contrast, you want to align the segmented detector such that the beam cone, which diverges downstream of the focal spot, just fills the quadrant segments (see Fig. 19). Note that for absorption contrast, detector alignment is not crucial as long as the beam falls within the sensitive area of the detector chip and you are looking at the bright field signal (sum of all segments) only.
You have to align the detector in the transverse directions (X and Y) as well as in the beam direction (Z) as described below. You should iterate a few times between the two, because the axis of the Z detector stage might no be exactly parallel to the beam, and therefore there is a drift sideways as you move in Z.
When you are done with the alignment, don't forget to record it in SM_GUI by clicking Alignment Edit Alignment Record Advanced Record Detector Aligned: SIDET.
The numbers given below for detector alignment (scan sizes etc.) are only rough recommendations - don't hesitate to play around.