Ah, The Old Man. That really was a fun game (and maybe the longest I've ever played). Thanks for the good time.
To the OP: James McMurray has really offered an excellent beginner's tutorial here, and the additional input from Skowza is also pretty helpful. Morale is generally the most fluid resource. In the most recent game I played (referenced by The Old Man, above), we ended with Morale at 2, but it was increased over the course of the game by at least that much. Certain crises and quorum cards (Inspirational Speech being the most obvious) increase Morale, sometimes through the trading of other resources and that is often very important, because very many crises hurt Morale. And since so many crises hurt Morale, if the fleet isn't managing its resources well (say you're overpassing Crises, for example), you'll feel it in Morale first. Generally speaking, you lose Fuel to jumping, Population to civies, Morale to failed skill checks, and Food to choices on Event cards.
So I'd suggest that it's less important how many Morale skill checks you faced (they are the most common, after all) than how many checks you overpassed and by what amount, compared to how many you failed. The trick is to find some way of bottling up that wasted value in skill cards and sprinkling a little of it over the other checks.
Finally, you're right about character selection mattering. It really does, and I found participating in this discussion on the topic to be instructive to me:
Hope this helps!