It is proven that the Prophet used to pray four Rak`ahs after `Isha’. As for the Hadiths which speak of the virtue of doing so, they are all extremely inauthentic; the best and strongest of them is the Hadith of Ibn `Umar, despite the fact that it is inauthentic.

It is Sunnah to make these Nafl prayers brief: 1. Two Rak`ahs before Fajr prayer 2. Tahiyyat Al-masjid 3. Starting voluntary night prayers with two brief Rak`ahs 4. Two Rak`ahs following Tawaf. It is Sunnah to make the following prayers lengthy: 1. The eclipse prayer 2. Qiyam Al-layl With regard to Sunnah prayers other than that, one should do what helps him be more focused.

If you missed Fajr prayer, but made it up after sunrise, then you may pray Duha because Duha prayer is a confirmed Sunnah that has no connection to Fajr prayer whether it was done on time or made up later.