Where do I find the manual to find out how to properly use (connect) warehouses?
No manual for this game that I know of. Mostly you learn from watching Youtube videos and/or experimentation.
I have learned how to use warehouses pretty well.
First off, while you can place them anywhere except inside a city, they will connect to anything they are next too and will automatically take from resources or sell to cities. Food for thought.
One important aspect I often forget is that if you send a good to a warehouse, you need to tell the WH to hold it. Small WH's hold 3 goods I think. While large ones hold 6. By default, they will hold only 20 of a good, but you can set it to 99.
As for uses, think of them repositories. Have a bunch of raw materials out in the countryside? Ship them all into a WH and then have some separate trains bring them into the cities. Stockpile for when a city grows and now you can ship in sugar. Attach to a big city where all the fright goes so you can run express lines into the city proper. And yes, any good used by a city are sold and paid for.
Hope that helps.