Probably the best way to think of it in this case is to "pull" the car (really meaning drive it) over to the side of the road and stop. Of course, idioms aren't always easy to explain, and to some extent they just have to be learned by rote. I can tell you that any language that I'm familiar with (French and German in my case) uses prepositions differently than they are used in English, and we preposition-users have to learn them by rote as well.
A well-known example is the French "à", which usually means "at", as in "je suis à la maison" for "I am at home" (literally, "I am at the house"). However, French also has "canard à l'orange" meaning literally "duck with orange". (We call it "duck à l'orange", a tip of the hat to the French origin of the dish.) For another example, the German for "I am at home" is "Ich bin zu hause", which is literally "I am to house"!
I give you this example so you will understand that it isn't just because your language doesn't have prepositions that they are hard to learn! Their use is idiomatic in many cases in other languages, too. We all have to study them one at a time when learning a different language.