Jeff is right, use the single |, this should do what you want, will die if the answer is not Y or Yes, otherwise just carries on. Just make sure you use warnings and strict

print "Do you want to submit Job A? ";
chomp (my $question = <STDIN>);
die "Goodbye\n" unless $question=~ /(yes|y)/i;
print "Are You Sure?  ";
chomp (my $question2= <STDIN>);
die "Goodbye\n" unless $question2 =~ /(yes|y)/i;
print "Everything good\n";
[download]

Hope this helps ...