I created a cargo container that has a deployable AFCS targeting system that will connect to this over the radio link. Once I clean it up I will upload to the workshop. With that, you won't have to integrate an AFCS TGTSYS into your ship. The downside is that you will have to go to the container to control the radar and weapons, however this would make it easy to just put on your ships and go.

I will also create some good instructions. A lot of the AFCS documentation is unclear, with examples that are equally unclear. For someone coming into it with no knowledge of how this works, its very daunting. Once you get the hang of it, it gets easier but boy is that a steep hill to climb and I deal with real world tactical data links.

how connect it to a cargo ship

There's a door where you will find the controls, you must connect it remotely to a AFCS compatible targeting system (like one on a jarrmarine ship)

where do I control it lol?

"Its just a cargo ship, its not like it can fight back".
Famous last words of someone that fell for the second oldest trick in the book.

dubious tactics shall be employed