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The effective stack is the number of ships that can participate in combat when one stack fires on another.
Fleets are made of 9 stacks, with up to 3000 ships each. However, during combat, only a portion of each stack will fight. The ships fight as if they had only the effective stack number of ships engaged, with the exception that shield points and hull structure points of the rest of the stack are in the common pool. Any active module that uses He3 is affected by effective stacking.
The star ranking of your commander determines your maximum effective stack size. This is perhaps the biggest benefit of high star commanders- using more ships in a fight. This means more damage dealt and more damage mitigation from defenses.
Standard Flagships such as the Independence and Black Hole have an effective stack of one of the main ship types, plus the Flagship bonus (100). The Independence is a Cruiser with the Flagship bonus while the Black Hole is a Battleship with the Flagship bonus. All Humaroid Flagships are Battleship type hulls with the Flagship bonus. At the time of this writing, Liberty wings is the Frigate based Federation Flagship, however due to game enigine limitations it had to be given -100 instead of +100 or it would have exceeded the 3000 ship limit in some circumstances.
Flagships based on Battleship hulls, like the Black Hole or any Humaroid Flagship, are best commanded with high Battleship Skills. The Independence is currently the only Flagship based on a Cruiser and is better commanded with high skills in Cruisers, similarly for Frigate based flagships (Liberty Wings). If both ships are used in the same fleet then the best commander is one that is rated at least B in both Cruisers and Battleships.
The new Tesla Flagships follow the same rules (For more on this see: Flagships).
You can use an existing Commander that is normally deficient in such skill ratings by enhancing that commander with gems. Notably, Battleship, Cruiser, and Frigate Diamonds of level III or higher.
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