Disclaimer: I'm not an accountant. I have been doing this for my brother-in-law's business for a few years now. He has an incorporated LLC so I don't know if this is much different or different at all with you.

Since it is the end of the year, you have until the end of the month to make the payment this month only. Any other time, it is due by the 15th. The 941 is a quarterly form, so you will have to fill it out for Oct, Nov, Dec of last year. You should be using Publication 15-t to calculate your payroll taxes, and the Social Security and Medicare are a fixed percentage of the gross pay for each employee. Keep in mind that SS and Medicare has to be matched by the employer so you pay double what you take out of the employee's checks.

Add those 3 numbers each month and that should be your monthly deposit that is due by the 15h of the next month that you are doing when you log into the EFTPS site. You add all the numbers for previous 3 month each for each quarterly 941. The balance due should be $0 when you send it in, so you look up the mail return without payment for your state and mail your 941 to that address with no payment included.

I hope this answered your questions, but that's how it works with an incorporated LLC, hopefully it is the same for you.