Hey Aaron,
There are a few ways to do this (we'll make this easier in the future). The best way to currently do this is to have the separate branches for beta / production / etc.. The branches will be represented by separate *.wys files. For example, http://yoursite.com/beta-updates/server.wys
Then you can either use separate client.wyc files for the separate branches or use the -server or -updatepath variables/ commandline arguments to let your users or your app decide which branch they're on.
Does that make sense?