It will not support Version 3 as yet. It will control whichever you have open out of SDPlayer, Winamp 2 or CoolPlayer. I believe MadIce is looking into adding Winamp 3 support. He is the creator of the DXPlayer plugin and also the SDPlayer itself which in my opinion is a great media player. It's not just a music player but a true media player and has support for plugins to control almost every aspect via objects using the DXPlayer plugin.
I have heard rumours that there is a plugin which allows Winamp3 to respond to plugins that control winamp2 but don't know any more than that I'm afraid.