Am I required to make up for the time spent going to prayer if I have agreed with my employer to work 12 hours a day?

You are not required to compensate the employer for performing the obligatory prayers and confirmed Sunnah prayers, as these are excluded from the employment contract. This includes the time for purification (Wudu/Ghusl), the prescribed (Fard) prayers, and the regular (Sunnah Ratibah) prayers. However, regarding going out to the mosque to perform the prayer, you must seek permission from the employer; otherwise, the prayer should be performed at the workplace.