Don't build your AA towers in the direct path the flying things take, it's better to have them farther away (but obviously still within their attack range) so you can attack for longer without worrying about them doing too much damage in return. That's where the repair and booster towers that Streeteh mentioned come into play.
Haven't played that game in a good couple of months actually, I'll have to get back to it soon. Got completely stuck on the level with the two bases that have to be defended, I keep getting molested on that one.