This has to be the dumbest question ever, but I am in the middle of the tutorial and I can't for the life of me figure out how to load troops on ships. According to the tutorial text blurb, and the manual, you just select your army and then right-click on a ship which must be in an adjacent sea zone, right?
well, when hovering over the ship (my army is 16 and located in Ulster and the 3 transports are floating in the Irish Sea), the cursor appears with an X which I guess it means it is unselectable; and indeed I right-click on it and nothing happens. Same thing when the ship is in port and appears as a this gear-y thing. What am I doing wrong?

It's not a dumb question, so don't worry mate.

Secondly, yes the navy have to be in the adjacent sea zone for you to load your troops onto it.

Here's the deal thou, you can't load land troops onto just any kind of naval vessels. You likely need to build some transport vessels, such as the Cog. As the other vessels are combat vessels. So remember to make sure that your transport vessels have some protection in form of combat vessels, as they're not really worth much in a fight.

I can't remember wether the transport vessels can carry 1 regiment per boat or not thou :-\

I only ever played EU 2, but there you had to have the ships in the sea (not in port) and the capacity of the ships had to be sufficiently large to contain the entire army. Maybe try splitting up your army in smaller chunks to see if the capacity is an issue?

You might be right I started with EU II (still have the discs including Asia chapters) ships are limited by size.

You all were right, the problem was the load capacity, my 3 transports were only able to house a size 6 army (2 per transport). I think I had read ingame that you could try to load an army of any size and that any excess troops were simply left behind, but that is not the case. The ordered army must fit into the fleet or they won't move at all.

Thanks everyone. Now, back to conquering those pesky mameluks ;)