Are you working with the native InRoads tools or are you working with OpenRoads horizontal and vertical geometry?
By your explanation, it sounds like you have a surveyed XYZ of the surface and you need to design the horizontal and vertical, correct? Have you looked at the vertical regression tools to get best fit vertical alignment created? You would need to create the horizontal and extract vertical regression points of the surface gradeline to get a best fit vertical.
As far as annotating and exporting the corresponding heights and offsets, once you have the horizontal and vertical alignment created, there are numerous reports for reporting station/offsets and clearance reports for comparing multiple elements.