"Kaisa, where is the car?"
Translation:Kaisa, missä auto on?
Basically, yes, though there is a slight difference. This difference could be expressed in English like this:
Missä auto on? = Where is the car?
Missä on auto? = Where is a car?
The latter example sounds like maybe a parent asking their child (Kaisa in this case?) to point to a car in a picture book, while the first sentence is used when the car is familiar, but it's location not: maybe Kaisa parked it somewhere unknown, or somebody stole it. The difference is slight, but noticeable, but I think you'd probably be understood by the context whichever version you use in any situation.
These are different ways to form questions. One is with the "-ko/-kö" ending when you want something confirmed. These questions can be answered with a yes or a no. You basically turn an affirmative sentence into a question with this ending. It can be added to many kinds of words, like verbs, adjectives or pronouns. "Onko sinulla kissa?" (Do you have a cat?) "Minäkö?" (Me?/I?) "Kissako sen söi?" (The cat ate it?) Adding it to a verb is probably most common; adding it to some other words sounds like you want to highlight that word a little. In English these questions are formed similarly with changing the word order ('do you' instead of 'you do'), or by adding a do at the beginning, or simply by adding a question mark at the end, which in speech can be simulated with the raising intonation.
The other way is with interrogatives, or question words ("kysymyssana" in Finnish), like "mitä" (what), "missä" (where) or "milloin" (when). These questions demand a bit more explanation in answer, a simple yes or no won't do.
So, "Onko missä auto?" is a bit weird construct. It's like asking "is where the car?"; one doesn't really know what is wanted in answer. Even so, you might hear this way of questioning in some parts of Finland (spoken language) even though grammatically it's not really correct.