1. Yes. An S-Corp has a separate filing from the personal return, Form 1120-S. This can be prepared and filed through TurboTax Business (which is only available in Desktop). The Form 1120-S will generate Schedule K-1, which will be used on your personal return. You can choose to use online software for your personal return, but may find features of desktop more advantageous for your tax situation.
2. No, what you describe is not payroll. Payroll is paying employees (including yourself), wages and or salary that will be reported on Form W2. Because S-Corp pass-through income is not subject to Social Security/Medicare taxes, the IRS has established a standard that shareholders (in this case, you) in an S-Corp must be getting paid reasonable compensation from the S-Corp. Otherwise, all of the earnings can be recategorized as wages and subject to appropriate Federal taxes. This requirement is even more strictly enforced now because S-Corp (pass-through) can also qualify for the Section 199A (QBI) deduction. You may wish to consult with a CPA to determine what reasonable compensation is related to your business.
What you are describing actually represents distributions. You pay tax on the company earnings when they are "passed-through" to your personal tax return. However, when you take distributions from corporate earnings, these are tax-free as long as you have sufficient basis in your corporation.
3. TurboTax itself does not track your business quarterlies. (If you have made personal estimated payments, TurboTax will have a record of what you set up during tax preparation last year). Quickbooks can track business expenses and employer-related tax payments. Depending on the subscription puchased, this information can potentially be imported into TurboTax.
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