In such a question, what is most commonly done by native speakers of English:
focus on the past action of you putting the car keys somewhere – somewhere not-too-logical-seeming?
Where did you put the car keys?
focus on the present result of me not knowing where the car keys are, of the car keys having disappeared from sight?
Where have you put the car keys?
Do the two questions differ in the degree of annoyance they might express?
(No grammar book or website I know of, and I know quite a few, is detailed enough to deal with such a point – apart from this website, that is! Flatter than flatter? Flatterer?!)