Many underwater applications that involve the use of autonomous underwater vehicles require accurate navigation systems. Image registration from acoustic images is a technique that can be used to achieve this task by comparing two consecutive sonar images and estimate the motion of the vechicle. The use of deep learning (DL) techniques for motion estimation can significantly reduce the processing complexity and achieve high-accuracy position estimates. In this paper we investigate the performance improvement when using two sonar sensors compared to using a single sensor. The DL network is trained using images generated by a sonar simulator. The results show an improvement in the estimation accuracy when using two sensors.