Yes, you'll need to file Form 1040X for each tax year that you need to amend, attaching your Schedule D and Form 8949 to the back. See Assembling Your Return in the IRS's Instructions for Form 1040-X for more information, and the TurboTax Help article How to amend (change or correct) a return you already filed for instruction on how to amend your previously-filed tax return.
When you have multiple years of amended returns, mail them all in one package, so that the IRS has them all together for input. Be sure, however, to plainly indicate that multiple years are included -- perhaps in a letter included in the package.
You can pay by check or money order, but there are other options, as well, described in Line 20—Amount You Owe in the link above. If you choose to mail a tax payment, make your check or money order payable to “United States Treasury.”
See Where To File in the link above to determine where to send the amended returns.
Generally, for a credit or refund, you have to file Form 1040-X within 3 years (including extensions) after the date you filed your original return, or within 2 years after the date you paid the tax, whichever is later.
