The confusion is in youir terminology using two sine waves.
Isnt it one sine wave . Unless your counting the primary coil as one sine wave and the secondary as another sine wave, both are the same sine wave appearing in two different coils. In which case the sine waves appear in phase with...
So the way i see it is by looking at two secondary coils beside each other with opposite polarities. So current travels from left to right in the first and right to left in the second.
Left coil left side is the bottom of the sine wave, and right coil right side is the top of the sine wave...