I'm still not sure I understand your problem but I'm going to take a stab at it anyway.
When measuring the door, you consider the 24 mountains. That's how you get S3.
Then, you demarcate the sectors as in the previous systems. All the S3 gives you is the distribution of energies. The chart is still divided up into 9 palaces and labelled in the usual sense.
For S3 Period 7, refer to page 50 in your manual. The chart has been adjusted so that the south sector is on top. Just copy the stars onto your house plan's sector. If south in your house plan is at the bottom of the page rather than at the top, then just note relationships/collaboration star in that sector.
Does that help?
Kaye
