2. Let's say I have twenty towns with barracks. How does it divide up the resources appropriately to those locations?
It will weigh several factors...what's being trained at a given moment, whos closest, whost connected via road, who may have top priority for a resource, etc. In the end, I would say 20 barracks training 'Magic Dragoons' is a bad idea if only one city can make 'Magic Dragoon Spears'.
3. How will the user be able to tell what their shipping lines are?
Roads are your user-defined shipping lanes. If you dont have a road, the shipment will take the shortest route. If you have shipments going over enemy lines, then you better have the military strength to hold that area while your caravan makes its drop.
Combine that with trade routes (if applicable), and this will truly require a good UI to manage that complexity.
I feel the beauty of this system comes from the non-necessity
of a complex UI: your actions on the main map (building placement, road construction, etc) will drive the distribution of goods. That's not to say we won't allow micromanagement types to tweak numbers themselves, but I see the automation to be pretty straight forward (and thus capable of doing a great job on its own)
I would say, if you have resources going to somewhere you don't want, then you need to re-examine what buildings are active in a given city.