What you're referring to is the "Prize Rules". In short, merchants could be stopped and inspected; if they were not carrying "contraband" (ie: war materials), they were allowed to pass. If they were deemed to be carrying contraband, they could either be siezed or sunk. If the warship decided to sink the merchant, they were required to ensure all hands were safely off the ship and into lifeboats, given a course towards land, and a notification made.
The Germans adhered to the prize rules in the first part of the war, but gradually abandoned them in favor of unrestricted warfare after it was determined that U-boats were in more danger from the merchants than vice versa.
This is a quick once over, there's much more to it than that.
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