Must the questioner make up the day she fasted with the intention of making up (a missed fast) and the six days of Shawwal, given that she was unaware of the impermissibility of combining them, and is she liable for an atonement for delaying (the make-up fast), knowing that she only learned about it in Ramadan and is unsure about her reaching puberty?

Fasting is not obligatory until the signs of puberty are manifest. If these signs have not appeared, then there is no obligation to make up the day that was not fasted, nor is expiation required. As for combining the making up of Ramadan (definition) fasts with the six days of Shawwal, this is a matter of scholarly disagreement, and some scholars permit it.