Give the first route one job
Use one cargo ship to move one material between a supplying station and a receiving station. Before automating the loop, watch the ship load at the source and unload at the destination. The official Main Sequence Steam page describes automated supply routes as the next step beyond running production inside one station.
Prepare each end of the trip
At the supplier, trace the material from production to the dock and check that enough is ready to load. At the receiver, trace the cargo from the dock to storage or the machine that needs it. Keep the first shipment small enough to see what happens on both sides.
If the ship travels but no stock moves, work backward from the failed transfer. A navigation success tells you the ship reached its destination. You still need to confirm that the stop transferred the item.
Repeat the loop before adding cargo
Configure the ship to visit the supplier and receiver in order. Watch the first circuit, then let the same trip run again. On the second trip, check whether the source has replenished stock and the receiver still has room for the next load.
Add another cargo type only after you know the original route works. If the new shipment fails, compare its loading and unloading behavior with the working item.
FAQ
What makes a good first cargo?
Pick a material that one station produces and the other needs. It should be easy to identify in both stations' stock.
Why does the ship arrive with nothing aboard?
Check the source dock and whether the intended material was available at the loading stop.
Should I automate both legs at once?
Verify the transfers separately first. Once you know both work, schedule them together and observe a complete circuit.