At my office, we like to arbitrarily call the Main Level Floor 100' so that when you go down levels, instead of moving -12' you move to 88', for example. Is there a way to set this up in the story levels so when you look at an elevation or section, the levels below the main level won't be negative relative to the Main Level?
Sure. Instead of moving story levels around, use reference levels to achieve this. For example, set your first reference level to -100', then in sections/elevations set annotations to use this reference level.