hope this helps....
1) If there is only enough time to read the two Farz of Fajr Salaat and not enough time to perform the Sunnat Salaat, then one should perform the Farz and later, after sunrise, make the two rakaats Sunnat with the intention of Nafl (as there is no Qaza for only Sunnat).
2) If,however,one missed the whole of the Fajr Salaat, then one should perform the Qaza before Zawwaal by first reading two Sunnat rakaats and then two Farz rakaats.
3) If Qaza is made after Zawwaal,then only the Farz rakaats have to be read.One should NOT read the Sunnat rakaats in this case.
4) If there is hope of gaining even one rakaat or one sitting (qadah) in the Farz of Fajr,then one should not miss the Sunnat rakaats,(i.e. read the 2 sunnats and then join the Farz.)
5) It is strictly forbidden to perform the Sunnat rakaats after the Farz rakaats BEFORE sunrise.
6) To recite Surah Kaafiroon and Ikhlaas in the two Sunnat rakaats of FAJR is proven from the Ahadith.However,one should not regard it as being essential and occasionally one should leave it out.
7) It is Makrooh to continuously recite Surah Sijdah and Surah Dharr in the two Farz rakaats of Fajr on every Friday.
8) If a person read four rakaats instead of two for the two Sunnat of Fajr, and then made Sajdah-e-Sahw at the end,then the first two rakaats will be regarded as Sunnat and the second two as Nafl.
9) On the entry of Fajr time,one should not perform any Nafl Salaat except the Sunnat rakaats before the Farz rakaats of Fajr.fill this simple commandment of Allah, cannot be overlooked.
(Ref: Fatawa Mahmoodia - Vol Two ; Ahsaanul Fatawa - Vol Three; Fatawa Rahimiyyah - Vol One; Nurul-Eezaa.)
In one Hadith,Rasulullah(S.A.W.) has stated:-
The two most difficult Salaats for the Munaafiqs (hypocrites) are the Fajr and the Esha Salaats.If they knew the virtue and goodness of these two Salaats,they would have attended it even if they had to crawl.(Bukhari).
Rasulullah(S.A.W.) has also said :-
The person who performs the Fajr Salaat with Jamaat (congregation),is under the protection and mercy of Allah Ta'aala . (Ibn-e-Majah).