Prepositions are difficult when you are learning any language: each preposition has many meanings, and the meanings don't overlap with those of prepositions in your own language. The only way to learn them is to look at the definitions and memorise the examples that you will find in a good dictionary.
Looking at in the car / on the car, you will find these definitions in the Cambridge Dictionary:
in: inside a container, place, or area, or surrounded or closed off by something
on: used to show that something is in a position above something else and touching it, or that something is moving into such a position
From these two definitions, it should be clear that, if somebody is sitting in the car, she is probably sitting in one of the seats inside the car. If she is sitting on the car, she is probably sitting on the bonnet (the cover of the engine compartment) or the roof.
Be sure to read all of the definitions, though, because on has other meanings that might be relevant, for example:
used for showing some methods of travelling
This is mainly used for public transport, and would not be used for travelling by car.