Looks like i'm one of the few that actually prefers naval combat to land. When controlling large groups of ships, your deployment is probably the most important part of the battle. With a bit of luck you should be able to deploy your ships so that when they are sailing in a straight line towards the enemy, the wind is fully behind them. This allows you to control the pace of the battle yourself. Generally when controlling 10+ ships, i give a move (not attack) command to a point past where the enemy ships are GOING to be. This does require a bit of estimated guesswork, but generally if you can work out the speed of the enemy ships and the direction of the wind your ships will intercept them. The ships will fire automatically, so all you need to do is give them a route which will bring them as close to the enemy as possible. If you are at an angle to the enemy, it is possible to sail in between two ships, unleashing a broadside on the bow of one ship, and another bow on the stern. Once all my ships have gone past the enemy fleet (and fired), i pause the game, and give them another move command. At this point i generally take direct control of three ships (taking control of three larger ships such as 3rd rate or above is actually easier than smaller ships, as their turning circle and move speed is slower, allowing you more time to reload, fire and turn). The initial attack has to be the largest, as once you have to turn round you no longer have the wind behind you, meaning that the battle is back on even terms.

One thing i never do is use the attack command, as the pathfinding is less than useless. Far better to use move commands and let your ships fire at will on anything within range.

I would say when attacking a fleet with a flagship or admiral, go for that one first. Take direct control of your two largest ships and send them after it. Once intercepted, you should be able to unleash four full broadsides within a matter of minuites. Crippling the admirals ship, just like killing a general, will give you the upper footing

Anyway, thats how i fight my naval battles. Thoughts?