Generals at Sea
As the concept of dedicated admirals didn't exist in Japan at this time, a general simply controls a fleet of ships in exactly the same way as he does an army. Simply order your general to board a fleet for him to take command. If your fleet does not have a general a commander will be assigned to it in the same way (and with the same restrictions) as if it was an army fighting on land.
Movement of Fleets
Left-click to select a fleet and then right-click to move it to any part of the highlighted area - this is the extent of its movement capability during a single turn.
Blocking Movement
Positioning a fleet in the straits between two of Japan's great islands enables that fleet to block other fleets from using that route and enemy armies or agents from crossing between the headlands by use of the land bridges that stretch between them.
Revealing the Map
Since diplomacy with and war against other clans can only be undertaken when your respective territories are adjacent, you can increase your line of sight by sending fleets further along the coast or agents into unknown lands to encounter new clans. However, be careful not to go too far without back-up - you may fall foul of hostile neighbours or suffer attrition if your ships stray too far from the coast.