Think of the RAM SS Layout type like a section through the whole structure. Any columns that are cut by the section should be modeled on that layout typically. Don't worry, the program will design the column for the correct, longer unbraced length so long as there are no beams (or optionally decks) at the intermediate story to brace the column.
There is one alternative, however. If the column is only modeled on the Roof, and not modeled on the lower level at all, then you can add a foundation under that column and lower the foundation to stretch the column to the full height. This approach can be helpful in cases where the column is sloped and the story heights are not constant making it hard to determine the exact bottom offset to keep the two-story column in one straight line.