In this paper, we investigate the influence of different loci of manipulation relations (position of the player's ability to assert control) on presence. Novel game input devices (such as Microsoft Kinect or PlayStation Move) contribute to presence, and allow a broad range of game interactions, such as using facial expressions, gaze or head movement. This increase of complexity has led to some interesting design challenges: in a typical game design the setup of the locus of manipulation is quite simple as there is only one. For instance, the player uses a gamepad to move a game character through an obstacle course. However, design decisions get more complicated, when a game design includes more than just one input device and a second locus of manipulation. Does the relation of the two loci of manipulation have an impact on the perceived presence? To address this topic we utilized eye tracking technology, and carried out a comparative study consisting of four scenarios based on a 2D platform game. Three scenarios are controlled using an eye tracking device and a gamepad. They differ in their relation between the player character and the avatar. The 4th scenario is solely controlled with the gamepad. Results revealed that the inclusion of gaze input to investigate this issue proved to be very effective. It was discovered that the relation between the loci of manipulation has a strong influence on the perceived presence and its sub-dimensions.