If you want to ask someone "Where did you park your car? "
You can say BOTH of them, because they are the same means.
However, " O-KURUMA wa Dochira Desu ka? " is more polite than Doko desu ka?.
(You should use "O-kuruma wa..." when you are in business scene.
However, if you are in other than business scene but you want to say politely,
You can use the phrase "KURUMA wa Dochira Desu ka?"
A case of with your friend, you SHOULD say just "KURUMA wa Doko? / Kuruma wa Doko ni Tometa no?".
When you want to ask someone "Which one is your car?" in a parking area or in a front of some cars.
"Dochira ga anata no kuruma desuka?"
"Docchi (If there are just 2 objects) ga anata no kuruma desuka?" (polite)
"Dore (if there is more then 3 objects) ga anata no kuruma desuka?" (polite)
"Docchi / Dore ga anata no?" to your friends.