There doesn't seem to be a standard way to do this. Looking through Google books, I found:
- a dash: “Where did you get your license—from a Cracker Jacks box?” (Christopher Meeks, 2005)
- a comma: “Where did you get your license, in some kind of government giveaway?” (Michael Fox, 2000)
- dual questions: “Where'd you get your license? A vending machine?” (Shirley Jump, 2013)
- an ellipsis: “Where did you get your license... in a Cracker Jack box!” (Joseph Santiago, 2008)
Even though all of those could be found in published works, scrolling through the results, the comma seemed most prevalent, followed by dual questions.
It seems wrong to make it two independent sentences, both ending with question marks
Really? You think so? That practice seems okay to me.