The AMCAS application wants to know about every grade you ever received. Therefore, unless the school removes your bad grade from your transcript like redstar18 said, the AMCAS application will average the two. This means that your AMCAS GPAs will be lower than your school GPA. This is common.
I'll give you a for instance. I just got my post bacc degree at Boise State University. They have a cool policy called "5 year grade replacement" wherein if you do below a C in any course, you can replace the grade by retaking the class within 5 years. The problem however is AMCAS (isn't it always?). They still require you to report both grades even if your school doesn't factor the lower grade into your GPA. AMCAS is a bastard this way. But hey...at least it evens the playing field.