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Get your taxes done using TurboTax
#(2) Yes if you have enough tax withholding taken out of the RMD you won't need to send in estimated payments. You only need to fill out form 2210 if you end up with a tax due when you file your tax return and owe a penalty on 1040 line 38 for not paying in enough during the year from withholding and estimates.
If you do not pay in enough tax from withholding and estimates, you may have to pay a penalty for underpayment of estimated tax. The penalty is an Estimated amount. Even if you are getting a refund you can still owe a penalty for not paying in evenly during the year. Generally, most taxpayers will avoid this penalty if they owe less than $1,000 in tax after subtracting their withholdings and credits, or if they paid at least 90% of the tax for the current year, or 100% of the tax shown on the return for the prior year, whichever is smaller. It is included in your tax due or reduces your refund.
#(3) The RMD has nothing to do with paying estimates or entering estimated payment you paid. And your other questions are completely wrong.
You enter the RMD from the 1099R you will get at the end of the year in January. Any withholding will be in box 4. You only enter it from the 1099R, nowhere else. RMD withholding will show up on 1040 line 25b from Forms 1099. Here is a 1099R to see box 4, https://www.irs.gov/pub/irs-pdf/f1099r.pdf
For #(4) You have to separate the RMD from the withholding. The RMD is the gross Required Minimum Distribution you have to take from your IRA or 401k account. You can have them take tax withholding out of the RMD. Or you can pay in extra quarterly estimated payments to cover the tax due on your RMD.
You don't actually pay the tax on the 1099R. You have taxes withheld like from your paycheck. You still have to enter the whole gross amount (before taxes were withheld) with your other income to figure out the total tax (and it may put you into a higher tax bracket) and then the withholding is subtracted from the total tax to figure your refund or tax due. The Gross amount shows up on 1040 line 4a or 5a and the taxable amount on 4b/5b. The withholding will show up on 1040 line 25b.
Hope that covers it and is clear.