That sounds an interesting project. Will your controller give the speed and heading of the boat, or the rudder and engine settings? Both approaches should be possible, using the UDP networking messages.
These are defined in http://bridgecommand.co.uk/Doc/networkprotocol.php
If you are controlling the engine and rudder settings, the boat's dynamics will be simulated in Bridge Command. For this approach, you'd run Bridge Command in 'Networked (Main)' mode, but instead of connecting to the 'Map Controller', you would connect to your own controller program, which would send 'MC' messages to Bridge Command via UDP. In particular, you would use the 'Engine and rudder failure record', using this to set the engine and rudder parameters.
Instead, if you are simulating the boat's dynamics yourself, giving speed and heading, you will need to use these to generate a current position in metres (relative to the South West corner of the sea area). You would then run Bridge Command in Secondary (3d) mode, and update its position by sending 'BC' messages to Bridge Command. You would also need to send at least one 'SC' message as well to set up the scenario.
Hopefully this and the documentation in http://bridgecommand.co.uk/Doc/networkprotocol.php should help you get this set up, but please ask if you have any questions.