After you pray Fardhs in jamaat, is it mandatory to change your position to pray Sunnahs? Why is it done?
Only Fardh should be prayed in Masjid, Prophet (P.b.u.h) said that do not turn your houses in grave by not praying at home. Sunnah prayer should be prayed at home. By changing position the person change place of prayer which justify Sunnah Prayer at Masjid.
When molana is reciting ayaats during Fardhs, are we supposed to be reciting something as well? What about in 3rd rakat when he is quiet?
According to Fiqh Hanafi, When one pray behind Imam He/she should not recite Surah Fatiha and Quran. The Qiraat from Imam is enough for every one no matter if the Qiraat in prayer is loud or with very low voice.
Is it mandatory to pray 2 sunnahs when you enter the mosque and before you take a seat?
The two sunnah prayer is Taheyat-AlMasjid. This is not obligatory if you go to the same masjid all the time. But if you go to a different Masjid then it is mandatory.
Can we repeat the same ayaat in all rakats or do they have to be different in each?
According to Hanafi Fiqh, Yes you can repeat the same Ayaat in all Rakats (if you only know that part of Quran) OR like people pray Salat- Tasbieh. Other then that if you repeat the same Ayaat then your Salaat will be completed but it something which is not liked (Makhrooh), It will not effect your Prayer but it is better that if you recite Ayat keeping the Sequence of Surah's and Length of Ayaat. for example if you recited from SUrah 5 in first Raakat then next Raakat should be Ayaat from a surah after that not from Surah 3 or 4.
It is the same reason even if you pray Ba'jammat at home, Until that place is used for something else or Mussala is folded that place will be respected and considered as Masjid.