This is what I use with Stuf and Dominos. Is this too hard for you to see? I don't use kgpanels or button facade at all. I too get tired of my UI so I turned to Stuf which gives you a lot of customization, you can do just about anything with the built in config. As for managing the addons, I for one have minion installed, don't really use it, if something breaks then I'll just check Minion for updates and let it do its thing, otherwise if I know what broke I'll just download the updates from the site.
Sounds like you're putting too much thought into the whole process.