When you amend a return and add a W-2, does it only show you the refund for that one W-2 instead of the whole total refund with the W-2s aready filed a day before?

Once you transmit your return you cannot change it or get it back.  You would have to wait until your return gets rejected or accepted. 

If rejected, you can make your changes or add information to your return.  

If accepted, you would need to amend your return to correct or add information to your return.

The federal amend form is set to be available on 2/11/2016. When you amend the counter will start back at zero and show the adjustment made by the amending forms.

https://ttlc.intuit.com/replies/3288565

Thank you so much for your help. This really gave me a better understanding of making an amend to my return. I just thought they took my whole refund and then i owe $2.00 but it actually means they'll take $2.00 out of my tax refund?

No.  You will get the first full refund and the amended return is only for the difference you owe or get back.

To make sure the amended return does not cause delay in your refund wait to submit the amend form until after you have receive your refund. Then you will just need to pay if you owe after the corrections.

Whoa, whoa, whoa!  You cannot "amend a return you just filed the day before--unless that return was rejected by the IRS and you then went into your account to include the additional W-2.  Is that what happened?  If not, and you just went in to your account and changed the W-2 information when you realized your mistake, that "amendment" went nowhere at all.  

If what you did was e-file, then realize that you had another W-2:

Now you have to wait until the IRS either rejects or accepts your return.  If your return is rejected, you will be able to go into your account and make the necessary changes to your income and re-submit your return.  If the IRS accepts your return, however, then you have to wait longer until it has been fully processed and you have received your refund.  THEN you can prepare an amended tax return and mail it in.  You cannot e-file an amended return.  They have to be mailed, and it takes at least a couple of months for the IRS to process an amended return.  Meanwhile, DO NOT go in and start changing anything on your return in the system, or you will make a mess for yourself.  Sit tight and wait until you see what the IRS does with the return you just e-filed.

I meant a couple days ago. It has already been accepted by the IRS.

Then see the answer already given above.  You now have to wait to make corrections by amending your return with a 1040X.  You will be waiting until mid-February to do that, when the 1040X form becomes available.