This translation is not English, unless it means "Where should one take empty bottles?". Otherwise, it would have to be "Where are you going with the empty bottles?"
No. A different Czech verb (jít) would be used if the English sentence was in present continuous.
This is not a good English translation. There is technically nothing wrong with the sentence, but it would not be expressed this way. A more natural translation is "Where do you take the empty bottles." or "Where do the empty bottles go?"