For your setting out - TREADS: centre as normal all the way down the stairs, then using a gauging staff, measure your best cuts and amount of tiles you will need. RISERS: Follow the lay of your treads, ensuring that you cut the row of tiles to the highest point of the tread (before the tread tiles are put down). If you have uneven stairs, then after you have fixed your risers. you may need to backfill with some levelling compound before fixing the tread tiles.
The tread tiles always sit on the riser tiles. If you dont have profiled tiles for your 90 degree angle at the edge of the step, then you will need to fix a foot strip on each step.
You may want to consider putting some movement joints inbetween the tread and the riser ( this can be a bead of coloured Silicon, but you can get produced fittings).
Hope this makes sense to you?