I file as a S-Corp, sole owner. What FORM NUMBER do I use to pay quarterly estimated taxes for the S-Corp? I assume I submit payment at EFTPS or directpay.irs.gov?

it's unlikely that the S-orp needs to pay estimates.   income passes through to the shareholder who is the one responsible for personally paying taxes on the income.

Why do you think the S-Corp needs to pay estimates? There are rare situations where it would.