Hi Munhwan,
To unregister the custom transport, just delete it from the deploy folder. When you refresh the Transports list in Manager, your custom transport will no longer be in the list.
Note that any inputs or outputs that used that transport will be in an error state after you delete the transport.
Also note that any connectors that you had created that used that transport will automatically have their transport re-assigned to one that does still exist. For example, I have a custom transport for RabbitMQ. I created a new connector that used the RabbitMQ transport and Text adapter. After I deleted my RabbitMQ .jar from /deploy, my transport was gone from the transport list (expected) but my connector was still present and was set to use the Feature Service transport. Most likely, if you're removing a custom transport or adapter, you will also want to delete any connectors that used that transport or adapter.
Lastly, to register a custom transport (or adapter), you do not have to do both steps you mention. You can *either* place the .jar in the /deploy folder manually *or* use the register in Manager, which just does the same thing. I personally always use Manager to register a new transport (or adapter). If you have an empty /deploy folder, try using Manager to register your transport. When you look at the deploy folder, you'll notice that the .jar is there.
Mark