The way I think of it is: The logistics system is somewhat like Advanced Tactics, but also somewhat not.
In AT, you needed to put trucks & trains in SHQs. Then the SHQs would move supplies and reinforcements to units. The SHQs would get the supplies directly from city production.
But now, the trucks & trains are trapped inside of buildings. You have to build those buildings (although your people may build basic logistics hubs), and you need enough workers for those buildings.
Supplies are also now split up into food, ammunition, oil, etc. Some of which are used a lot more in combat, such as ammunition. Furthermore, all production buildings need to pull their resources from somewhere - no more instant transfer of metal & oil like in Advanced Tactics.
So now units & buildings are competing for truck & rail points. In the long run, you want to use rail stations in all cities and rail stops at all exterior buildings, so that enough truck points are left for units going off-road. The penalty for distance from the nearest road is also harsher - in Advanced Tactics you could go quite far off-road in open plains, certainly not in Shadow Empire.