I think Anti-Ship missions are setup as they were before NA. Barring the 'Pr'mary target' bug mentioned in another thread.
The shipping routes are defined in the Terrain Movement file, you list a start/end area and the coordinates of waypoints.
Now with the NavalMap=TRUE, the colors in a watermap only are in effect in Single missions, which will place carriers/transport groups randomly for a Naval Strike mission. This is my understanding.
Because in campaigns you already define your naval groups in the campaign_data file, their start and final objective points. As TK mentioned in a thread today, the naval group will sail at their set speed and the game will calculate their movement even when you are not flying. So he says the naval group will move as much as the whole map distance in 1 or 2 days! They take a straight course from start to finish..
That's why he kept the NA campaign so short, a few days...
I hope I'm not leading you the wrong path, Jonathan might give more insight here, since he's released a few campaigns using these parameters.