Do you input quarterly estimated taxes on both forms 1040 and 1120s? Do you input 1099-misc forms for a business on both forms 1040 and 1120s?

If the 1099 MISC is in the name of the business, it gets entered on form 1120 S only.

Quarterly estimated tax payments are entered on form 1040 only.

The S-Corp does not pay income taxes.  The earnings of the S-Corp are distributed to the shareholder.  So, the income is recorded on the S-Corp return.  It is distributed to the shareholders after expenses are deducted on form K-1.  The shareholders must pay tax on the distribution.  Estimated tax payments are made by the shareholders to pay for the taxes due on S-Corp distributions.

You said "Quarterly estimated tax payments are entered on form 1040 only." Check form 1120S, line 23a, 23d asks for 2015 Estimated tax payments.  Is this the same Quarterly Estimated Tax payments also entered on my 1040? Thx

You said "Quarterly estimated tax payments are entered on form 1040 only." Check form 1120S, line 23a, 23d asks for 2015 Estimated tax payments.  Is this the same Quarterly Estimated Tax payments also entered on my 1040? Thx

You can only enter them once - either on the personal return or on the 1120 S.  If you paid them they belong on your 1040 only.

OK. On form 1120S, line 23a, 23d, what are 2015 Estimated tax payments used for? The 4th Qtr payment is also due 12/15 each yr, instead of 1/15 each yr.

where on the 1040 are the actual estimated payments entered?

In Turbo Tax Business  (2019), When I entered the estimated quarterly Tax paid in S Corp Information Worksheet , Part III , For some reason on Form 1120 S Section 26 " Overpayment " TT business automatically refund entire amount you entered in S Corp Information Worksheet , Part III. Why is it happening?

As a work around, I am leaving S Corp Information Worksheet , Part III as zero.

Any guidance will be much appreciated. 

It is EXTREMELY RARE for an S-Corp to pay estimated taxes (which is why there is a place for them in the business program ... if you enter them there then expect the IRS letter that will come)   so  NONE are entered on the 1120-S . 

They should have been made in your SS# and are entered on the 1040 only. 

FYI ... on both tax forms there are many many lines you will NOT use and you do not need to enter anything in those sections of the interview ... not even a zero.  In fact a zero is usually not a valid entry and will produce many error messages. 

The 1120-S has NO tax liability so there is NO reason for it to have paid estimated taxes which is WHY they are being refunded in full ... think about it.   The tax liability is being passed thru to the shareholders and that is why you paid personal estimated taxes.  Once the K-1 from the corp is entered on your personal return you will need those estimates there to offset the tax liability on the 1040. 

@Critter-3  Thanks for the explanation! 

When S corp pay IRS following on behalf of employee:

1. Quarterly returns ( Form 941) which includes estimated Federal Tax withheld from employee, Medicare & Social Security
2. Annual Return FUTA Tax (Form 940) 
3. Any State Unemployment Tax (This doesn't goes to IRS)

I understand employee can deduct estimated Federal Tax , Medicare & Social Security reported on W-2 and Form 941. What about FUTA tax and State Unemployment Tax ? Who deduct and/or report those taxes? S-corp on 1120S  or employee on 1040. ?

Note: On 1120 S Form , under Payroll deductions, I already deducted employer's portion of medicare, SS , FUTA and state unemployment taxes. Thanks

You are mixing up INCOME taxes with PAYROLL taxes ... the corp pays payroll taxes on the payroll tax forms  NOT on the 1120-S.  An S-corp will never owe INCOME taxes ... those are paid on the personal return.   Payroll taxes are ONLY deducted on the corporate return.  

When S corp pay IRS following on behalf of employee:

1. Quarterly returns ( Form 941) which includes estimated Federal Tax withheld from employee, Medicare & Social Security   The gross wages are deducted + the employer's portion of the FICA taxes not just the 941 totals
2. Annual Return FUTA Tax (Form 940) 
3. Any State Unemployment Tax (This doesn't goes to IRS)

These are ALL corporate deductions on the 1120-S along with the wages paid.

I understand employee can deduct estimated Federal Tax , Medicare & Social Security reported on W-2 and Form 941.   NO ... an employee cannot deduct them ... the W-2 is entered in the program and the wages & withholdings are  placed on the correct lines of the 1040. FICA taxes have never been deductible on a personal return.

Note: On 1120 S Form , under Payroll deductions, I already deducted employer's portion of medicare, SS , FUTA and state unemployment taxes.   That is what you are supposed to do. 

May I suggest you seek out a local payroll company or bookkeeper to be educated on these matters if you don't get an A HA moment soon.

@Critter-3  Thanks for your feedback.