"How long do we stay?"
Translation:Wie lange bleiben wir?
It's not in third position; it's in second position where it belongs.
wie lange? is one unit and takes up the first position of the sentence - you can't split it up.
Compare English, where we say "How long do we stay?" and not "How do long we stay?" or "How do we stay long?": "how long" is a single unit and cannot be split up.
"Positions" in a sentence count not by individual words. A group of words that has to stay together will count as a single unit.