I've never played Britain, which I guess really lives from trade, so I'm not too sure about this, but from my understanding, the Shipping Boxes work pretty much like the Shipping Box in Civil War I & II.
A faction which has transports, or merchantmen, in a shipping box will earn money (WSU too?) through trade each turn, or every few turns; I believe I read that somewhere.
If you want to mess with an enemy faction's trade, put some raiders into a Shipping Box where he has trade ships. Aside that they might attack the trade ships, their presence, will reduce their trade income from those trade ships.
There is a Blockade Box, but only one. I'm guessing, but I imagine that it's only useful for the Brits to blockade France, but I'm not sure, and I don't imagine it would work otherwise.
You can also Brown Water Blockade not only coastal harbors, but also harbors with coastal waters as their river front, by stationing enough combat ships in the ocean if from of the harbor and/or river mouth.
For example: park enough British ships in front of Rochefort, and they will not only blockade Rochefort, but Bordeaux as well.
This is going from what little I've read about it, and extrapolating some from CW.
Edit: Storms etc. hell yes, ships at sea are affected by bad weather

Best way to keep them on station, is to rotate them per need. Check their cohesion. I believe they can receive supplies from ships in the trade boxes, but I'm not too sure.