I'm at the part where you have to defend the flagship against waves of attacking zeppelins carrying hordes of soldiers. I'm playing on Hard difficulty, so enemies soak up enough damage that I can't quite keep up with them, and they slowly destroy the ship's core. (I don't even want to think about dealing with this on [1999 Mode][1]...) 

What strategies are effective in this fight? Should I be saving my "air strikes" for the gunships, or should I be using them against the infantry on the decks? How do I deal with the Patriots?

  [1]: https://gaming.stackexchange.com/q/110653/274