wyBuild to test server

I must be missing something with the instructions on pushing an update to a test server. I am trying to push a patch to a test server so I can test a few computers (myself and beta testers) but I don't want to push an update to the main user base.

I created two download sites, both on the same domain but in different folders:

http://myapp.com/updates/%file%http://myapp.com/updates_test/%file%

Then I created two sites on the upload the updates section pointing to the same two folders. My main updates have worked fine for a while now. But I recently tried to push an update to the test folder and I think it updated both. I assumed highlighting the proper Site in the update would push only to that folder but it seemed to do both. I ran a simple bat command in my app's folder:

wyUpdate.exe -server="http://myapp.com/updates_test/wyserver.wys"

And it updated me to the test version. Unfortunately so did the normal check for updates embedded in my application (from another machine).

Did I do something wrong?