Get your taxes done using TurboTax

Okay I got that taken care of and filed. I got back a refund on my Federal return and efiled it through Turbo Tax. Then today I forgot about a Carpenters pension and received another 1099R so I filed a amended return and ended up owing. I never had to amend a return and when I got to the end Turbo Tax said my taxed were filed and accepted. That is for the first time. How will the IRS know I now owe and will be sending in the amount from this amended form?