Step 1. Move your boat to a shore (not in the see or ocean).
Step 2. Move your foot units that you want to be transported to the land square right next to your boat.
Step 3. Move those foot units to the square of the boat and you will be loaded. Just move the boat to another place then unload those units be choosing the unload button. Or you can just switch to the unit by right clicking. But that boat or whatever have to be on a shore or else your unit won't unload.