I don't like using the Navmap either, because freezing time to take stock of the situation feels like cheating.
But the comms chatter is helpful... whenever confed pilots note new incoming waves (e.g. "enemies inbound, pick your targets," etc.), I take a few seconds to do a fast-cycle through all the targets and take note of any bomber silhouettes. Sure, it takes a few seconds - and that's precious seconds on the clock while the Grikaths get their torpedo locks... but if you don't like using the Navmap because it spoils the action, this way works well enough most of the time.
Saving the Verdun isn't too hard if you pay attention to when wave 2 shows up. The Sao Paolo, on the other hand... geez, that situation's worse than Kurosawa 2. Kurosawa 2 is a 50-50, if you afterburn in the whole way and continuously taunt all 4 (or 5?) Gratha into attacking you during the whole dogfight. I'm sure someone here's managed to save the Sao Paolo (and some braggart is going to claim that it's easy even on Nightmare), but I haven't managed it yet.