If you have an LLC with an election to be treated as an S corporation, then that entity is a pass-through to the shareholders (who receive a K-1 (1120-S); the S corporation does not pay federal income tax except in unusual circumstances.
As a result, the shareholders may need to pay estimated taxes and can do so by printing and mailing Form 1040-ES or using one of the payment sites run by the IRS.
See https://www.eftps.com/eftps (requires registration)
See https://www.irs.gov/payments
