Currently in a game at the minute (legends of Revolution Mod)
I always have normally 3 vessels in a self supporting triangle at least one sailing turn + a couple of extra tiles sailing from my coast along the suspected line of attacks from major AI worries (normally at least one will have sentry promotion), so I can see incoming attack fleets.
Behind the screen I will have groups of attack ships normally a fleet of 3 in each location which will be just less than 1 movement turn from the next attack fleet.
So basically I sort of work out were enemy fleets should come from, screen fleet can give a short advance warning which allows me to pull in the other attacks fleets and hit the incoming in a short sharp blow.
As the vessels improve and get longer travel movement the screen go out further and the attack fleets moves out etc . A few subs later on help for roving look-outs or trailing fleets. Once airships , aircraft and later on UAV's are available enemy surprize attacks are quite hard to pull off unless their are staring within a very short travel time. Or you forget to recon the sea with the aircraft ( have forgot many many times


Oh for a set patrol route for air units)
That said if they manage to slip past as MontyZ just did to me sent 2 fleets, one fleet 10 ships= 7 galleons, 3 frigates which I found and pulled by counter fleet to engage,(while not at war but he was coming for me) so I struck first. But Monty had also sailed a much larger fleets 20 ships around a mutual friends coast and popped out near my coast, and landed on MY ISLAND (the cheek of Mad Monty)
However I had managed to get 3 frigates up-graded to escort Cruisers
attack Str 22 movement 5 so none of the enemy fleets ships made it back to Aztec land (WW1 or early WW2 type ships against wooden ships was fun for me)
To sum up:
1. Sail in groups to help support each other.
2. Have other groups close to form large fleets quickly
3. Never let empty or full transports escape if possible
4. Scout most likely attack routes.
5. Tact

incoming fleets works a treat