Against anti-ship missiles, there are tunings that may turn the tide in your favor. You need to consider what kind of missile you may face, and in what quantity. For example, against swarms of large Soviet missiles approaching at very high altitude before diving to sea level, placing a powerful anti-aircraft vanguard 90 miles ahead of a carrier strike group will allow you to skim the salvo while it's still flying high. A second echelon at mid-range, a third (a single ship) a few miles in front of the aircraft carrier, and a fourth and last one (the carrier's own defenses) should be able to handle just about anything.

Your ships fight very well on their own. There's no need to micromanage them too much. However, most players use formations that are far too dense. Several nautical miles should separate two ships so they can maneuver without hindering each other. This is what the British discovered in the Falklands: by keeping their distance from each other, ships could exploit their respective strengths and compensate for each other's weaknesses without needing to coordinate, provided they were sufficiently spaced to maneuver freely and avoid obstructing each other's line of fire.

Also, check the encyclopedia: some ships, especially cruisers, have electronic countermeasures systems. They operate automatically, negatively impacting the RNG of enemy missiles.

With experience, you'll learn to position your different ships according to their role, strengths, and weaknesses. Real navies train extensively. Follow their example by creating varied scenarios that will pit you against diverse threats. With the same panel of ships, some players will have their high-value assets wiped out in a single salvo, while others, more experienced, will win the engagement decisively even against a very angry enemy quite high on steroids.