I have efiled my return and it has been accepted and I filed for an extension because of a missing 1099-r, if I have received the 1099-r do I amend the return?

[xmasbaby0]

You have done some confusing things.  If you already e-filed there was no need to file for an extension.  But if you have now received a 1099R that was not entered on the original return, then you can amend that return.  See below.

[xmasbaby0]

When your return has been fully processed you can amend it to add that 1099R.  Read through the instructions for amending before you try to make any changes to your tax return.

 Go to  Federal> Wages and Income>Retirement Plans and Social Security>IRA  401 k) Pension Plan Withdrawals to enter your 1099R.

https://ttlc.intuit.com/questions/1894381-how-to-amend-change-or-correct-a-return-you-already-filed?...

A 1040X cannot be e-filed.  It must be printed and mailed.  It will take about 3-4 months for the IRS to process an amended return.  It is a good idea to use a mailing service that will track it, like UPS or certified mail, so you will know it was received.

Wait about 3 weeks from mailing and you can check the status of your amended return:

https://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1

https://www.irs.gov/filing/individuals/amended-returns-form-1040-x/amended-return-frequently-asked-q...

https://ttlc.intuit.com/questions/1908543-do-i-need-to-amend