I personally have different fleets supplying my warehouses. Either set in the port itself or inside the supplying trading fleet.
There should be a feature to set a limit of how many resources a warehouse should have.
Example:
Port A has a limit of 20k cotton. Fleet Cotton keep supplying cotton until 20k is reached. From that point on the fleet sells the cotton, until there is less than 20 again.
Would be something to help avoid situations, where warehouse got filled with 100k cotton but only has 2k tools.