Generally you are right 'on' is for something or someone over something else and 'in' is something or someone inside a place or object. If you stick with that rule you will use those words correctly more often than not. However, even though you ride in a bus it is more correct to say "I'm on the bus." because that is just how we refer to big transportation vehicles when you don't control it ("I'm on the plane now." "I will be on the train tomorrow."). For smaller vehicles you say 'in' ("I'm in the car." "I'm riding in the limo to the party."). For things usually 'on' and 'in' are very specific if one object is physically on top of another then use 'on' if it is inside the other then use 'in'. "My keys are on the table." "My shoes are in the box." etc. Apologies for not being more specific. I hope this helps. Keep learning :-)