I agree that this can be confusing at first. It looks like you've got your reference levels set probably correctly, but once you do that, you can use the elevations in your project the way the site elevations are actually labeled. (i.e. if you are doing a terrain, then the elevation points will be just like the topo survey says.) Think of the reference levels as an alternate way to view the absolute elevations. Project zero is always the same, but can be labeled alternately in reference to other benchmarks, which then gives you an alternate place to enter the elevation relative to project zero. If you set Sea Level to -100' below Project Zero, PZ will be either 0, or 100' above Sea Level, depending on where you want to enter the information. The program doesn't really care. This is for YOU, not the program.
However, I'm not sure why you've set the terrain mesh so low initially, or why you've added another story for the survey.
Richard
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Richard Morrison, Architect-Interior Designer
AC26 (since AC6.0), Win10