Charged Missiles

Charged Missiles is useful for destroying groups of enemy units from long-range since Charged Missiles deals area damage and gives a range boost. This is very useful as it kills groups of enemy units much faster. Generally its a good idea to turn it off auto-cast.

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.

Throw in a couple of subverters to mitigate shields and stop a bunch a frigates in their tracks.  Maybe have a Devastator Cap ship fire off a nano machine shot and then have your changed missles do the rest