Crusader Kings II
There is a button on the Army screen that says "Disembark" click that when an army is in the same province as a group of docked ships that can hold the entire army.
You should be able to land troops.
The way to do it is to select your ships, and once they are selected, you should have a summary on the left part of the screen. In that window, there should be a small tab with a picture of a soldier on it.
Clicking on that should select your troops on the boat, and those should be able to move to any nearby land province.
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