I have just realized that as an International student, I must file 1040NR and not the 1040. In the process, I have claimed Work Pay credits in my previous refunds which I am not eligible for.

1. I originally entered the country in 2007 as a student on F-1. Should I file 2012 as a non-resident alien?

I have appropriately filled out the necessary 1040X, 1040NR, 8843.

2. My question is can I make a payment to return the excess money online though the IRS e-pay website?
3. If so, do I need to include anything other than the amended forms when sending in to the IRS?

2012 is your first year as a resident alien.

Ask that all penalties and interest be waived for each amendment.

Mail a separate check for each amendment for the added taxes owed.

If penalties and/or interest are assessed, the IRS will bill you