The big advantages to below decks autopilots are their, speed, power, and durability. This makes them more responsive and more effective than wheel pilots. Speed is particularly helpful when sailing down wind in a following sea, below deck pilots can keep up with the constant course changes, wheel pilots can not.
An additional advantage is the ability to follow the wind and not a compass course. Following the wind lets the AP work less reducing energy consumption and making for a smoother ride. Following a route with an AP is bad navigation for a couple of reasons. First, the AP will change course without warning when it thinks it is at the way point. Second route following does not incorporate any consideration of the actual conditions at the waypoint, is there another boat there? is the buoy off station? is there debris in the water? what are the sea conditions? etc.
The downside to below deck APs is the cost and complexity of the system and power consumption. The system requires a computer, an electronic compass, rudder position indicator, control head, and a drive unit. Newer models do not want a simple flux gate compass, they want a full on position sensor that includes pitch, roll, yaw, and compass heading.
Ideally the AP's computer will smoothly integrate with the chart plotter. This usually means the AP and the chartplotter are of the same brand. It may be possible to have a mixed marriage of brands between the plotter and the AP, but that may require some tinkering with the network. The same issue will arise if mating NMEA 0183 with a NMEA 2000K network.
AP computers are typically brand agnostic to instruments and sensors, like speed and heading, if the sensors are using standard NMEA data. They are also agnostic to the drive units, since the drive unit runs by changing the polarity of the power feed by the computer.
When making the decision on which system to install, begin with the Chartplotter and find an AP that is compatible with the chart plotter. Be aware, this can lead you down an expensive rabbit hole. In the end you'll have a nice fully functional system.
