Thanks Wnhough.

I was not able to reply to your answer, so I am opening a new thread.

I stay in Texas where there is no state taxes.
However I work in a state where there are taxes.

For estimated taxes, I have paid my federal taxes and state taxes for that state where I work.
Should I not be paying my estimated State taxes, since I live and my S-Corp is based in Texas ?

I have already worked for 4 months this year on LLC without generating my payroll, if I use quickbooks now to generate my pay checks retrospectively, am I in trouble with the IRS ?
Thanks

For estimated taxes, I have paid my federal taxes and state taxes for that state where I work.=======>>>>>>>>>>>You need to pay taxes to the state where you work as you earn taxable income there as a nonresident of the state.
As there is no state income tax in TX, you need to claim your taxes paid to the state where you work on your federal return by itemizing them on 1040 Sch A.UNLESS you itemize your deductions on your fed return, you can’t claim taxes paid to another state. when the tax liability is less than the taxes paid. You can often get a tax refund on yourr income tax if the tax you owe is less than the sum of the total amount of the estimated taxes thatyou paid, plus the refundable tax creditsthat you claim. (Tax refunds are money given back at the end of the financial year.)

Should I not be paying my estimated State taxes, since I live and my S-Corp is based in Texas ?=========>>>>>>>>>as mentioned above;it depends;aslongas you are subject to estimated taxes, then yes you must pay them to IRS/state where you earn the table income.your s-corp is a pass-through entity. It does not pay income taxes. The shareholders pay income tax(including estimated taxes) on the profits of the corp. These income taxes are paid only one time. If the corporation is paying you wages, as in payroll, taxes (federal withholding and FICA) are withheld from the paychecks. The withheld taxes are sent in to the IRS, and the corp also matches the FICA withheld from your check. ALL of this (the gross wages + the FICA matching) is deductible to the corp. In effect, this lowers the amount of income that passes through to you (but you are still taxed on the W2). These wages are not taxed twice, either. Your S-corp does not pay federal estimated income tax as the profit is taxed on your 1040 thru sch k1 of 1120S. You should use form 1040ES to pay personal estimated income taxes.
Note; Federal payroll taxes withheld are reported to the IRS on form 941, usually quarterly but may be monthly if large payroll . Payment of payroll taxes are usually paid to the gov through your bank with a payment coupon. You will also have a quarterly state unemployment tax and an annual Federal 940 tax. The S-corp is required to anually file a Federal 1120s tax return and the state returns.

I have already worked for 4 months this year on LLC without generating my payroll, if I use quickbooks now to generate my pay checks retrospectively, am I in trouble with the IRS ?========>>>>>>>>>>>>>>>>No;Aslongas you should generate your pay checks(aslomngas your get paid by the S corp as anEE/owner)retrospectively, your S corp , as a Texas employer is also subject to state unemployment (SUTA) and other TX payroll taxes, federal unemployment (FUTA) tax, and their share of Medicare and Social Security taxes to IRS; however,
Payroll taxes are late once the date for their collection or submission to the IRS has passed. Penalties for late payroll taxes are computed by multiplying the amount of the late payment by a percentage that is set by the number of days late. The penalty is 2 percent for taxes one to five days late. It increases to 5 percent from six to 15 days late; the penalty jumps to 10 percent for taxes late by more than 15 days.for TX payroll taxes you need to contact TX dept of Rev.

ok, so I did some more study on the taxes that needs to be paid as you said.
I formed the LLC and was of the opinion that I will elect as S-Corp by filing form 2553 at tax time.
However it looks like I have to file the below, some quarterly as below :
1120-W - estimated taxes for employer
Form 941 Employers QUARTERLY Federal Tax Return (PDF)
Form 943 Employers Annual Federal Tax Return for Agricultural Employees (PDF)
Form 940 Employers Annual Federal Unemployment (FUTA) Tax Return (PDF)

Since I am already past the deadlines, is it better to file 2014 taxes as SMLLC (not as a S-Corp) and then file as S-Corp starting from 2015 , considering the penalties by IRS ?

However it looks like I have to file the below, some quarterly as below :
1120-W - estimated taxes for employer===========As said previously, your s-corporation is a pass-through entity. It does not pay income taxes. But the S corp files a form 1120S to show its profits and or loss for the year.you, as an EE/ The shareholder, pay income tax on the profits of the corporation on your 1040 (thru sch k1 of 1120s);so as your S-corp is brand new and never was a C corp(and has no taxable BIG corp) , then it generally won't owe income taxes of it's own;however, you need to pay excise taxes to TX whrere the S corpo is .

Form 941 Employers QUARTERLY Federal Tax Return (PDF)=====>>Correct;
Form 941 is Employer's Quarterly Federal Tax Return. It's filed quarterly even if you have nopayroll taxes to report.

Form 943 Employers Annual Federal Tax Return for Agricultural Employees (PDF)========>>you need to File Form 943 if you paid wages to one or more farmworkers and the wages were subject to social security and Medicare taxes or federal income tax withholding .


Form 940 Employers Annual Federal Unemployment (FUTA) Tax Return (PDF)
==>>>>>>>..as said,you have no employees (but yourself, if Iyou aRE cconsidered an employee) and you do not pay myself through payroll (say youn simply pay bills and then pay youreself whatever is left over each month, which is never very much).
you need to file Forms 940, 941and your state employment tax returns as well. As a corporate officer IRS requires that you pay yourself a reasonable salary which is subject to employment taxes

Since I am already past the deadlines, is it better to file 2014 taxes as SMLLC (not as a S-Corp) and then file as S-Corp starting from 2015 , considering the penalties by IRS ?=>>>>… The election can be canceled by the LLC at any time. Once the election is canceled, the company reverts to an LLC that is taxed as a smllc or sol e ownership then you had to pay quarterly estimated taxes on the taxable income generated from the biz.due dates are apr/jun/sep/ dec 15 2014;if you are filing as a sole proprietor, and/or a self-employed individual, you generally have to make estimated tax payments if you expect to owe tax of $1,000 or more when you file your return.