If you have already filed your taxes, you should wait and get your refund before you do anything.  If you try to do something now, they might get confused and hold your refund unnecessarily.

 The IRS knows clerical errors happen and that people send tax forms late.  Since all companies are required to send a duplicate 1099-R to the IRS, it is probable that the IRS will notice you have left off a form.

So, wait to get your refund, and then file a 1040X on paper with the IRS.  

All you need to do is update the form with any figures that change as a result of the additional income.

However, if any of your schedule attachments change, you must complete the entire schedule again. Most importantly, be sure to include a copy of the 1099 with the amended return and include a payment for any tax you now owe. If you are still awaiting a refund from the original return, wait until you receive it before filing Form 1040X.