Put your ships in a sea province adjacent to a land province with your troops in it. You must have 1 transport ship for each regiment to be transported.
When they are adjacent, select the troops and right-click on the ships. The troops will walk out onto the ships. It takes them about two weeks to board, and when they are boarded a little tab will appear on the upper right of the ships' unit box showing that it has ground troops aboard.
When you get where you are going, if it is a friendly port, just dock and the troops will automatically unload. If it is an assault, reverse the loading process by stopping adjacent to the land you want to assault, click on the ground troops tab on the ship box to select the ground troops, and then right-click on the province you are assaulting.
