"I simply had the company make a makeup payment through EFTPS in February when the mistake was realized."

What was it identified as: 941? 1040-ES? Whose ID was on it: Yours? The S/C Corp? An LLC?

"we were making our one yearly withholding payment in December, but didn't realize that it was wrong until February."

There really is no such thing as "wrong" as far as income tax withholding. You can pay $0, for instance, through payroll, as long as you paid in whatever is required through ES or other means, such as carry over refund from the prior year.

"I am doing the taxes for the company now and want to issue W-2's to us so that we can file our personal taxes after the company taxes are filed."

An amount paid in 2022 is not a 2021 tax payment. Are you getting some professional guidance on this, or are you asking the internet, without giving us enough details?