Read the rules of general combat very carefully.
Remember also, “As many hits as possible must be assigned”. (General Combat, Step 3). It clarifies here as well with an example that submarines cannot hit air.
This essentially answers a lot of questions for you… if you had destroyers and submarines firing you’d want to seperate these out because it may be a case that the submarines score hits against a mixed force including air and you will need to know exactly what hits assign to what, according to sub/air rules.
The presence of the destroyer takes effect at the start of the rolls… so if a destroyer disappears, submarines special abilities that would otherwise be cancelled kick in.
This is always interesting when the carrier or battleship is the last surface ship… so it could end up being a costly casualty if the opponent has still got a surprise strike up his sleeve.
I think this adds a lot ot the gameplay, as there are often very tough decisions to make :)
Again this is all clarified in the general combat rules. Just read them carefully.