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.

Like the rest of the game, you are supposed to aimlessly click around, and hope you learn something. A sad state of affairs for modern gaming. Most developers have a F em attitude toward the people who buy their products. Which is exactly what get with Railway Empire. You pay money to be totally disrespected.

I learned how to set a warehouse up somewhat but I didn't know you have to ship it by train into the city?
I noticed that after I shipped some goods to a warehouse the goods did slowly disappear, so I figured the city it was connected to took it themselves?
trying to practice in free mode, so I imagine I could ship goods to the warehouse from the city it is connected to as well?
you gave me another train of thought to try with, so I am off to try that.

when you place a warehouse next to a city and the warehouse is green, you want the blue line that appears between the city and the warehouse. That mean this warehouse is now connected to the city. So set up the warehouse to accept whatever goods you want and then when they arrive at the warehouse the city automatically takes them as required.