Since the dashboard forces you to always have at least 1 'enabled', the only work around that I have come up with is to use the TAG method. The SSID isn't being broadcasted so it technically serves the same purpose =P So you would not have to do anything special after that since it won't be 'on' per say.
The whole template system has always been confusing to me so I honestly tend to stay clear of it. I don't have hundreds of sites, so I really don't mind making a new site from scratch or using the cloning feature from existing and then tweaking from there. Really doesn't take that much time.
If I did have hundreds or more sites, then I would bother mastering the template feature. Until then though, I will work by the sweat of my brow.