I really recommend looking at the help menu (on the pause main menu). Last subjects on the list regarding "workshops" are the ones who give info about settlements.
Not to be that guy who tells you to look at the manual, but that actually helped me.
Supply links can be from anywhere to anywhere as long as it connects to a chain. It shares abstract water/food resources (not items), therefore you can have a single settlement supplying water for many others. On items, yep, it only shares the junk section (so you can go to any connected workshop and open the menu, then press T on the PC to store all junk items at once).
The problem with having a single settlement supplying food/water everywhere is that the amount of defence will be absurd to guarantee that it never gets attacked.
On sanctuary, for instance, that could mean you get to the size limit by plopping many turrets and generators.
And producing surplus is really useful when you don't have time, patience, or want to just play. You can make a settlement with just 1 dude (provisioner), a bed and one or two turrets.
Of course, surplus food and water also gets deposited on the workshop, but I don't know how exactly this works. For some reason, Sanctuary always stores more Corns than Tatos, even though production is the same. Maybe they are insane and like the Tato taste, which reportedly tastes horribly.
E: About inventory management - what I do, is I have a shop, a drop-box and a rare-and-unique-loot-drop-box on my "core settlements" (most central ones on the map).
I'm really OCD about time-scale being insane, so I try to always fast travel to the nearest "core settlement" to dump stuff. Then, once I have patience, I sort and sell it.
Or I don't and magically get rich anyway, because that Luck Perk helps a lot!
They really should give us a way to connect containers, though. Everything should be accessible, the game is already time-consuming as it is.