The Holy Site is for you to gain certain army bonus and placed at certain locations on the map unlike some structures that are placed in every capital. It currently offers buffs on attack, army load and march speed. Choose one you would like to use the most which effect will last for 8 hours. Level 7 site requires you to send 100K troops minimum. The lower levels of sites will require lesser number of soldiers with lower buff percentage. Once the buff is chosen and the troop is sent, they will go to pray. I usually send 100K troops for that 25% buff and they pray for 1 hour. I am not sure for a troop that is smaller than 100K. Only one buff can be activated at a time. If you wish to activate another buff, the process of praying will have to start all over again.