You should recite Al-Fatihah with a subvocal recitation in the two Rak`ahs you are making up for. The two Rak`ahs you are making up for are considered the end of your Salah according to the preponderant view of the scholars.
Q 3: If I miss the first Rak`ah of the Fajr (Dawn) Prayer, is it permissible for me to recite the Qur'an in a loud voice in the Rak`ah that I perform as making up for this Rak`ah?
You should recite Al-Fatihah and any verses of the Qur'an in a loud voice in Fajr (Dawn) Prayer when you are making up for the Rak`ah you missed. (Part No. 6; Page No. 416) May Allah grant us success. May peace and blessings be upon our Prophet Muhammad, his family, and Companions.