We are traveling from Milwaukee, WI and connecting in Miami on to SXM. For the origin question, do I list Milwaukee or Miami? For the flight number do I list the flight number from Milwaukee to Miami or the number from Miami to SXM?
I think the form reads "originating" not connecting, so in your case it would be the first leg of flight (Milwaukee). We don't live in MA but we'll fly out of BOS so that's what I listed along with that flight #. But, then our flight is direct from BOS.
So perhaps SXMScubaman is correct in his posting. Also, he's seldom wrong in his advice.