the Messenger of Allah used to dismount at Dhu Tuwa and stay there overnight unitl he prayed Subh when he was approaching Makkah. The place where the Messenger of Allah prayed was on top of the big hillock and not in the Masjid that was built later on, but it was lower than that, on top of the big hillock.  

أَنَّ رَسُولَ اللَّهِ ﷺ كَانَ يَنْزِلُ بِذِي طُوًى يَبِيتُ بِهِ حَتَّى يُصَلِّيَ صَلاَةَ الصُّبْحِ حِينَ يَقْدَمُ إِلَى مَكَّةَ وَمُصَلَّى رَسُولِ اللَّهِ ﷺ ذَلِكَ عَلَى أَكَمَةٍ غَلِيظَةٍ لَيْسَ فِي الْمَسْجِدِ الَّذِي بُنِيَ ثَمَّ وَلَكِنْ أَسْفَلَ مِنْ ذَلِكَ عَلَى أَكَمَةٍ خَشِنَةٍ غَلِيظَةٍ