Can you post some more pictures so we can better understand the various elevations?
It looks like the top step of you climb out is above the water line, is it? If so how were you planning to finish that.
The bottom edge of your tile should be at least 3" below the waterline (typically this will align with the bottom of the skimmer opening), but nothing prevents that being a bit lower. One thing to watch out for is that it can get very awkward for the plasterers if the tile is too close to top of a step or your tanning ledge. They need an inch or two to leave a nice radius on the finish.
Also one recommendation: tile the top surface of the wall between the cover vault and the pool. The smooth tile surface will give the cover a nice surface to slide over as it opens and closes.