I am self employed with an LLC that I elect to pay S-corp taxes on. I am the only employee. When you're self employed, if your taxes are greater than $1000, you have to pay quarterly taxes estimated from 1040 ES.
I also have to do payroll every quarter because I pay myself a salary, and with that I have to pay the IRS the income tax, medicare, and social security that I withhold from my pay check. This amount only comes out to a little less than my 1040 ES taxes.
My question is, how do I handle this? Do I just have to pay the difference on the 1040 ES (i.e. if I paid $2000 on 941 and had $2500 due on 1040ES, do I just pay $500 on 1040ES)? Suppose my 941 came out to more than I estimated in 1040ES, would I have to pay it at all? How do these two forms relate to one another when you run a single employee LLC?