Yes, it's fine. I would probably say something like, "Where do you usually keep it?" but "Where is it usually?" sounds natural to me.

I agree with Lisa and Nicole. "Where do you usually keep it/put it?" is probably the most likely set of words I'd say. But where is it usually? sounds ok too.

I agree with Lisa, I would probably say "Where is it normally?" or "Where do you usually keep it?" Then move into something like "Where did you last see it?" or "Do you remember when you last used it?"