Learn French: Nous préparons le repas ensemble. - We are making the meal together.

You simply keep the exact same word order and add a question mark at the end in writing: Nous préparons le repas ensemble ? When speaking, you raise the pitch of your voice at the very end of the sentence on the word ensemble. This is the most common way to ask a Yes/No question in everyday spoken French.

Why is préparons translated as "are making" instead of "make"?

French doesn't have a separate "are doing" form like English does. The single present tense verb préparons can mean either "make" or "are making" depending on the context. Here, "are making" sounds much more natural in English.

Doesn't préparer normally mean "to prepare"?

Yes, but in French, préparer is the most natural verb to use when talking about putting together or cooking food. While you can say "to prepare the meal" in English, "making the meal" is what we would typically say in everyday conversation, which is why it is translated that way here.

Should I pronounce the "s" at the end of repas so it connects to ensemble?

No, there is no spoken connection (liaison) between repas and ensemble. The s at the end of repas is silent, so you just pronounce it as it normally sounds, followed directly by ensemble.