This is what I do:

After ordering them to attack, press Alt and then click on one Assailant, that will select them all. After you do this, click the ability button. Note that I am not sure if they will all use it at the same time. If they do, hurray! you're done. If they don't, use Tab to cycle each Assailant individually and press their respective button. Tab cycles to the right, Shift+Tab cycles to the left. You can see wich ship you selected because its background in the empire tree is highlighted.

Note: I generally let the AI decide who to attack, because I generally do not focus fire. If you focus fire with Charged Missiles you are wasting it. If you focus fire you eliminte the target quickly, but only a portion of the enemy fleet is affected. What you want is the whole enemy fleet affected by its AoE damage (those green lasers running between enemies).Your other ships can then mop up. Autocast must be off.