As other replies have said, I think of the scene sections the writing software uses similarly to scenes in a movie- the individual parts the story breaks into.
One thing that confused me for a while is the difference between the scene and the Scene, mostly because they use the same name.
Jim's blog has two long entries on Scenes and the follow-up unit of story telling the Sequel. I will add the word Unit to them to help differentiate them from scenes. A completely different nomenclature may be even more helpful (Conflict-Emotion?) but lets just use the words Mr Butcher used.
I wasted a lot of time trying to fit my story into Scene Unit-Sequel Unit pairs and then into the Chapter-scene mechanic of Writewaypro (very similar to scrivener).
Your story will probably use Scene-Sequel pairs but they may not follow the physical mechanic of separate scenes in your writing software. For example, your hero may be trying to get information from his cop buddy, but fails (Scene Unit). THe hero quickly rethinks a different approach (Sequel Unit) and tries it on the cop. This time the hero succeeds. (Scene Unit)
Another example (Spoiler from Dead Beat)
Jim shoots Corpsetaker inside Anastasia's body and then he argues with Morgan that it wasn't Anastasia. He can't force Morgan to back down (Scene Unit- Jim fails to convince Morgan to stand down). Then there are a few introspective paragraphs where Jim thinks through the sitiuation from Morgan's perspective (Sequel Unit-rethink goal, and then try something new). Then Jim tries a different tactic. This all takes place in one section of the story.
All of the above would be in one section of writing in your software.
Most writing software will put a separator (either an additional line or ### or ****) between the scenes.
Hopefully I haven't confused the issue by bringing up another usage of the word scene.