If it was me faced with this I would

1. Run a third quarter payroll

2. I would not date any official payroll checks for earlier quarters.. all returns would be late at this point and face penalties

3. As far as making a journal entry for QTRs one and two S Corp distributions aleady taken. how much are they?  if minimal I would leave them as S Corp distributions.  If subsantial you can do a deduction on your 3RD quarter paryoll. in essence credting S Corp Distribution as part of your payroll entry.