For indicating location, the general rule in American English is to use the preposition “in” for being in an enclosed or circumscribed space, “on” for being on a surface, and “at” for being at a point in space.
“In” is idiomatically used in these cases: “The children are [
in the kitchen,
in the garden,
in the car,
in the library,
in the class,
in school]. This is in the context of “kitchen,” “garden,” “car,” “library, “class,” and “school” as enclosed or circumscribed—but not virtually closed or insulated—space.
On the other hand, it’s idiomatic for native American English speakers to use “on” for being in these particular means of transport: “They are [
on the plane,
on the train,
on the boat,
on the submarine].” This explains the usage of “on” in this sentence regarding work on a submarine: “One of the typical duties of a Seaman Subfarer is working with non-nuclear divisions
on the submarine.”
However, for indicating an action, activity, or process that happens inside fully closed vessels, “in” is the idiomatic usage, as in this sentence: “Previously there were fears that women were more at risk from a build-up of carbon dioxide
in the submarine.” It’s in this same context that “in” is used in this sentence: “The vinegar was fermented
in big batching tanks.”
In contrast, to indicate being located at a particular point in space, the preposition “at” is idiomatically used: “She was [
at home,
at the library,
at the office,
at school,
at work] when we arrived.” The context is that these locations are not reckoned as places but as simply a point—a small dot of sorts—in space.
We must keep in mind that these indicative preposition usages are essentially conventional, even quirkish at times. They have no inherent or discernible logic of their own but have simply established themselves over time as the preferred usage by native English speakers.
FURTHER READING: Lesson #8 – Specific Rules for Preposition Usage