Either, it depends on the context.

The first is much more natural and the one you will be taught at any good school, or by any good native or fluent teacher. "is under the car" or is under/on top of beside X etc. We use like this "My dog is under the car" "My ball is on the roof" "Your dog/cat/coat/husband/wife/boyfriend etc is in the river" "There is a man under the/a car" reporting witnessing an accident. "A dog is under the car" is good only for witnessing and reporting an accident. To inform a driver not to move yet because of a dog under the car. we use "There is a dog under the/your car" For un specified dog etc. "There is a X under the Y"

Both are natural but it depends on the context of the situation. In some cases, both can be used all the same. For example... "Stop! Why? There is a dog under the car" "Stop! Why? A dog is under the car" In this case, either could be used naturally. So it really depends on the context. So in what context is it used?

Both are natural but it depends on the context of the situation. In some cases, both can be used all the same. For example... "Stop! Why? There is a dog under the car" "Stop! Why? A dog is under the car" In this case, either could be used naturally. So it really depends on the context. So in what context is it used?