Since they revamped the stair tools in Revit 2013 and tweaked them slightly in 2014 and 2015 we've had two annotation tools, Stair Path and Tread (or Riser) Number, to place view specific stair annotation.
Sadly the Stair by Sketch method of creating stairs is not recognized by these relatively new stair annotation features.
You'll find Revit is unresponsive when you attempt to apply them to your stair. They only work with Stair by Component. However, we can create a Stair by Component and then use Convert to turn each run/landing into a sketch based component and the Stair Path and Tread Number tools continue to work.
I assume this limitation has something to do with built-in locations within the component stair elements to define where the annotation can appear. There is no way to provide equal representation within the sketch. For them to work on the sketch based stairs I imagine it would be necessary to add another type of sketch element like Stair Path and/or RiserTread Path, like we already have for Run, Boundary and Riser. Using Convert on a stair component allows for sketch based modification but retains its componentness, at least enough for the annotation tools to keep working.
For now it may suffice to start with Stair by Component and then use Convert to modify the sketch as required. Worth a try.