Good for you for catching it before year end!

Here's how I teach payroll and S Corps:

You can take one annual paycheck, or quarterly or monthly or whatever, and still be in compliance. But I recommend not taking distributions as often as payroll or in lieu of payroll.

Here's how I would work through it:

The point here is paycheck date is never backdated now (since you are in the same calendar year), because as was pointed out, that makes everything late. For end of Sept, pay the wages that are for Jan-Sep. Date it for the end of Sept, because that is the reality.

Here's what the paycheck should show:

Everything taken as distribution turns into Loan to Shareholder (asset) to be recovered in this first and subsequent paychecks by net pay (out of takehome, not affecting taxes) deduction. That might mean "grossing up" the amount, because there should have been tax deductions and withholdings, and the company needs to be able to afford to pay its share of taxes, too. So, it's going to depend on how financially healthy is that bank account. Don't end at less than $0, of course, for the takehome amount.

You can even do this over the course of the remaining paychecks in the year. Example:

I took $12,000 already. I would like my paycheck to be $1,000 a month, so I'd like to be paid for Jan to Sept as $9,000 now, but after deductions, that might only be $7,500 takehome, and I need at least $500 takehome as funds. That means this first paycheck, the end of Sept, is grossed up so taxes compute and I am left with $7,500 and then we deduct $7,000 against my shareholder loan.

Now I still owe $5,000.

At the end of the year, whatever is left of Shareholder Loan can be considered distribution or still to be repaid in the next year, depending on how you view the data against Reasonable Compensation.

If you just ignore the distributions and move on to Payroll, you run the risk that payroll looks unreasonable next to the amounts already taken, which really should have been taxed through payroll for the most part, anyway. Again, it depends on the financial health of the business and perspective. I had a client who would take "loans" through the year, because her contracts didn't settle until the fourth quarter (her business was Summer seasonal), and then we would do an annual year end paycheck (including fringe benefits like personal use of company vehicle). Her distributions were 1/10th of her final payroll, but she claimed she was never sure through the year how the year would end, so she handled her uncertainty with minor cash distributions, then a big paycheck at the end.