Learn English – “Why the Sky is Blue”

You only need the question mark once, at the end of the sentence. While the two clothing items are separate, they're considered together in this context. "do you prefer the blue dress, or red shirt?"

The suggestion by Gary's Student to use bullet points is a good one.

If the questions must appear inline for some reason, you can number them instead:

Before we can examine the implications of neuroscience for criminal law, we must address two more fundamental questions: 1) Why do we punish criminals at all? and 2) How severely should we punish them?

With a longer inline list (perhaps three or more questions), use semicolons to separate the items. For instance:

Before we can examine the implications of neuroscience for criminal law, we must address four more fundamental questions: 1) Why do we punish criminals at all?; 2) How severely should we punish them?; 3) To what extent must punishment emphasize rehabilitation?; and 4) Should the family circumstances of criminals be considered when sentencing?

The semicolons aren't necessary for clarification, but they encourage the reader to consider each point more thoroughly by slowing down their reading of the list.