Originally Posted by zero-kill
You uncheck the addon from the character selection screen. There's a drop-down menu on the top left corner of the addons window that allows you to switch characters.
Unless of course you're wanting something called a Profile. Then you can set the profile within the addon options usually, save your current one as something and then change it for the Main.
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His problem is that the addon only allows lua configuration, so its unlikely that profiles are supported, even though that is what he wants.
Having 2 copies of the addon, while annoying, would fix the issue, but you'd have to be sure to have only one enabled at a time. The only way to do that, would be to change the .toc of one copy of the addon to register itself under a different name.