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Sorry I am a complete newbie to this game, but I have I believe a "logical" question:
Would it not make sense to manually target 1 particular ennemie unit using all available means rather than let units individually decide where to fire?
Sincerely,
JAG
It does, thats why it works that way for the most part. There is some degree of "intelligent" targeting as your ships try do do the most damage to particular types of ships they are effective against, but when you have your ships or fleet selected, right clicking on an enemy wil focus fire everyone in range on that poor sod 
Yeah usually all your ships if they are in a fleet will target the same target. You can also do it manually to make sure if you have the time. But you should know what ships do most damage to what units.
Many thanks, I really need to read up on my vessel table then! I have to say I am not finding this game easy at all, but where is the fun in something easy!
To clarify a little, ships of the same type will attack the same target. 
For example, all your light frigates will usually go for enemy carriers first, while all your long range frigates will tear the enemy's light frigates a new one.
Basically ships pick their auto-attack target by their attack type and the enemy's armor type, whichever armor type they get the most bonus damage against is what they auto-attack as a priority.
The table for the damage bonuses/penalties against various armor types is in gameplay.constants in GameInfo so you can peek at it with notepad. You'd have to look at each ship entity file to see what damage they do, but then it's also displayed in-game on their info cards what they're good against so you should get a good idea without having to dig in the files too much.
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