So, using the example given in your question, you would say
Wrapper submissionOne = new Wrapper("perl awesomebot.plx 042 045 0 324 432 6");
int guessTwo = submissionOne.prompt();
Wrapper submissionTwo = new Wrapper("python wonderbot.py 042 045 0 324 432 6");
int guessTwo = submissionTwo.prompt();
// Do whatever you want with the guesses