Its not as weird as it looks, but there are a lot of gear changes that make it confusing. The core system is actually quite simple, but the narrative elements make it look more complex than it is.
It is also key to focus on asset movement and applying traits and momentum etc as the core of combat, rather than the dice rolling. In most systems, movement is just an optional preamble and the interplay of the fight is in the cut and thrust of dice rolls. In dune, the movement and point spending is the cut and thrust, with the dice just determining the victor in a single roll (usually).
Zones- these are defined by the GM, depending on what they want to do and how complex they want it to be. Lets take the alley skirmish for instance.
GM 1 just wants a simple fight so decides there are two zones - ‘Market end of the alley’ and ‘Deep end of the alley’ representing the end of the alley the PCs first come into from the market, and the deeper part of the other end of the alley. Basically the zones are just the alley cut in half.
The GM starts most of the bandits in the deep end of the alley but a couple are waiting to ambush as the PCs arrive and are in the market end.
GM 2 wants a lot of tactical movement and conflict. So they break the alley into more zones with a little more flavour. ‘The dark part of the alley’ and ‘the alley near some steps’ and ‘the alley near a house’ and ‘the entrance to the alley’. The PCs enter the scene in the ‘entrance’ zone, but the bandits are scattered across all the others.
The GM can also apply different traits to each zone that will affect the conflict there. It might be dark, slippery, even trapped.
You can move between zones with an action and so the GM also needs to define where the ‘joins’ are. The 2 zone option is simple as they are next to each other, but more zones might be more complex. The 4 zone option might be placed as a square so they they link to each other, or in a line (like a long alley) meaning you need to move across other zones to get to where you want to go.
You can also decide to just use one zone ‘the alley’ , meaning anyone in the fight can attack anyone else.
If your character is in a zone they can attack anyone else in that zone. Ranged weapons can let you attack someone in another zone. Remember these zones are not specific measurements. All that matters is whether you are in a zone or not, where you are in that zone is irrelevant. People move about in combat - a lot- and so anyone can get to anyone else in a zone.
Making an attack is an opposed roll. The defender makes a roll to set a difficulty, the amount of successes they get being the difficulty for the attacker (no successes makes you an easy target!). The attacker then tries to equal or beat that difficulty.
If the attacker makes the roll the defender is out of the fight. No hit points, no mercy. The moving and interplay of traits and assets is the fight. Making an attack roll is more of an attempt to make a coup de grace on your opponent having found a weakness.
You may find your are looking for more complexity than is there, which I know I did when I first saw it. There is a lot of narrative freedom to determine what zones are and what any attack might represent. But the entire system of any combat is essentially:
-Move to the same zone as your opponent
-make an attack (use asset) opposed test when you have
-if you make the roll the opponent is defeated.
What changes from conflict to conflict is the scale and scope.
In warfare, zones might be different land masses you are placing tank or troop assets on. In an intrigue the zones might be people you are influencing with assets of blackmail or favour.
The rolls are the same either way. But in warfare a win means destroying enemy tanks and taking control of an area, in intrigue it is forcing an enemy to capitulate to your demands.
Does that make more sense?