Learn German: Sind Sie im September nach Spanien geflogen?

In German, all months are masculine and require an article. When talking about when something happens, German uses the dative case. The preposition in merges with the dative masculine article dem to become im. You will always use im for months!

Why does the question start with Sind (are) when the English translation says 'Did you'?

This sentence is in the spoken past tense, called the Perfekt. Most verbs use haben (to have) as their helping verb, but verbs that show physical movement from one place to another, like fliegen (to fly), use sein (to be) instead. The German structure is literally 'Are you... flown?'.

Why use nach Spanien for 'to Spain'? Could I use zu instead?

You should use nach. In German, nach is the standard preposition for 'to' when traveling to cities, countries, or continents that don't take a definite article (like Spanien). zu is usually used when going to a person or a specific building.

Why is geflogen (flown) pushed all the way to the end of the sentence?

This is standard German sentence structure. When a verb has two parts, like the helping verb sind and the past action geflogen, the helping verb stays at the front for a yes/no question, and the main action word gets kicked to the very end of the sentence.