I'm not sure I understand. If you are doing WDS, the SSID (the name of the wireless network) should be the same on both base stations. As long as the ATV is set to connect to the correct SSID, it will pick up the strongest signal it can for that network.
Your message implies that you have different names for two networks (assuming one for each base station) because somehow you know that the ATV is connecting to the old base station. With WDS, you wouldn't be able to know that (unless you're specifically checking the connected clients in Airport Utility).
Can you verify that you have a single SSID for this setup?
Steve