Autopilot and Sonar are operated through the FishDeeper mobile app. There is no limit to the number of points (points of interest) you can save on the map within the app. You can instruct the Autopilot of the Deeper Quest to navigate to any of those points.
You can also select a rectangular or square-shaped area on the map, and Deeper Quest will automatically scan that area with its sonar and build a depth map.
Additionally, you have the option to create a path of points on the map for the Deeper Quest to follow. The limit of points in this case is 999 (in other words, there's essentially no limit).