Hi Jaded,
1. Like in vanilla Civ, health comes from various plant bonus resources that you build bonus improvements on (dew collectors or plantations), augmented by buildings in some cases (like the water cache). You need to research techs like desert trade and more in order to get them connected (in Dune Wars tiles don't need roads to connect them to your trade network, but do need some early game techs).
2. Some buildings provide health directly, like the Mushtamal or (late-game) the hospital.
3. Don't stress if you have some negative health in the early game. It slows your growth a little, but doesn't halt it, you can still have excess water > unhealth.
The civs play at least somewhat differently, though we're still working on increasing their differentiation a little.
Fremen are the most different; their melee units can enter desert tiles on their own without transports.
Most of the other factions play reasonably close to each other, but have various UUs, unique resources and some UBs.
Also check out the leader traits; some traits have strong synergies with particular strategies. The Ixian Mechanized trait boosts Mech units and vehicles for example.
There are also quite big differences from using Arrakis Paradise civic or Arrakis Spice civic. Pick one of these, and don't change it; abandoning it can have severe consequences (all the civic specific buildings are lost).
Feel free to ask any questions you can't figure out, but do check the ingame Duneopedia, and the descriptions of the various religions (the different religions are quite different from each other in their effects and their spread mechanics) and new mechanics.
Hope you enjoy the mod.