Deductions & credits

Thanks to all the experts helping out on this.

I use the desktop version of TT premier. I manually checked the 50/100% boxes. The full amount of my deductions (up to 100% of AGI) showed up on Schedule A. TT DID NOT make the notation on the dotted line of Schedule A line 11 as Publication 526 calls for. The 100% deduction carried forward to Form 1040 and I had zero taxable income. I got the same letter from IRS limiting my deduction to 60%.  The question is, what do I do now? Do I need to file an amended return? Will TurboTax lead me through that?  I did not sign up for the TT audit support.   Thanks a million for expert replies.