As of Archicad 16, sea level is part of the new Project Location dialog box. (Options -> Project Preferences -> Project Location)
The sea level value is the elevation of project zero in the real world, which is usually the framing floor of the main story of the building (Story 1). This value is entered as a positive number in Project Information.
It gets automatically copied as a negative number to the Reference Levels, where it is locked and only for display.
With sea level set correctly, you can build your site model mesh using sea level topo data. Level dimension texts have autotext elements that can refer to sea level. Our standard story level markers and elevation marker objects can refer to sea level or project zero.
If you change the actual elevation of the project, you need to recalculate the sea level value and change it.
Sea level and the other reference levels are only for display and input assistance. Elements are always placed relative to their stories and project zero. If you change sea level, you don't have to worry about your site mesh moving around, even if you used sea level values to set it up.