Ok I'm gonna see if I can help out on this one (which is rare ;D).
Do you mean you want to be able to see where the boat is heading? If so, it'd be best to have the camera behind the boat. I'm not sure how the port is set up either, but if you come down from the hill to the port and see the boat coming into port, you could use camcommit 0 to change the camera position behind the boat immediately and use camsettarget to target the boat, rather than whatever is behind the boat.
As for the transition, you can cheat here ;D. Since you black out, nobody can see what is really happening, so you can do it pretty much any way. The easiest way that I can think of to do this, is to deletevehicle your first boat (once the screen is black of course) and create a new empty boat and use setpos to put it exactly where you want. You can place a new dude wherever you want by doing this too.
Copying units to the right place is very important when you want the intro to reflect the mission. An easy way to do this is to drag over everything you want copied, and before you switch over to paste it, focus on one unit and notice exactly where it is on the map (use a tree or bush as a reference or something that is on the blank map). When you paste it, everything is still selected, so you can move it as one thing, and you can click back and forth from mission to intro without deselecting it. This way you can switch back and forth until it matches up just right.
Hope this helped!