Done a few more missions, got invaded by Pharaoh in one again and had to re-start, but I'm getting the hang of it more now (at least on normal difficulty, not even tried the harder settings).
The main thing seems to be finding a really effective way of making money. Gold mines are great if you have them, then you just literally mint the coins, but usually you need some sort of trading, and many places have frankly shoddy natural resources. My last city basically set itself up as a flax processing centre, I had two docks, a bunch of storage yards, and about six weavers along the banks of the Nile, importing flax and exporting linen (occasionally also exporting beer, which was literally the only local thing I could produce and export from the raw materials).
My other problem was that it turned out I was too nice. It turns out that it actually pays off in many missions not to bother with housing quality until the late game - focussing on concrete mission objectives first (usually, building a monument of some kind, and supplying the rest of Egypt with whatever Pharaoh has decided on a whim that you ought to send them, even if it's something you have no way to produce) then only once that's complete bothering to supply pottery or beer to your poor starving townsfolk to get your culture/prosperity ratings high enough to win.
Next mission is building the first true (aka non-stepped) pyramid
