After you file

So it sounds like you did NOT enter everyone on ONE return and that you submitted your return before adding your second W-2?.  If you did not enter everything on ONE return, then you WILL need to Amend your return in order to add everything.  When you file a return, you only file one.  It does not matter which order on that ONE return you enter your forms, but they all have to go on ONE return and the numbers are added up together to come up with your total income and your total tax liability. 

After you start the amend process, you will go to the W-2 section and then select Add a W-2.  This is UNDER the summary box. 

You should only submit ONE return every year, which is the 1040 form. The ONLY time you should submit more than one is if you are correcting the first one but then you will use the 1040-X NOT submit the 1040 again. 

Having to amend your return, will likely change your refund amount. You may have to pay back some or you may get more back.  It just depends on how the additional income affects your overall situation. 

How to File an Amended Tax Return with the IRS