You don't have to pay anything because you are under company sponsorship they pay the fine
your QID date is the same date when u enter in Qatar but if ur company doing this late they put the same date for example.your date is 25/2/2013 but ur visa stamp on 03/06/2013 ur QID date is 3/03/2013.and ur QID expire on 3/03/2014 after that date u change ur sponsership.i think you may be understand some what