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I think everyone does this in their own way. I like to separate user settings and plugins in different folders inside the lua folder. And every plugin has its own config (setup, mappings, ...), so I can enable/disable them in a single place. My dots look like this.
There are numerous way you could go about it, I like to have the configuration of each plugin in its own file and invoke that in my packer startup, for example this would be my plugin configs files: https://github.com/jemag/dotfiles/tree/master/neovim/.config/nvim/lua/plugin-configs , each being invoked from packer : https://github.com/jemag/dotfiles/blob/master/neovim/.config/nvim/lua/plugins.lua
I keep plugin configurations in my lua/user/plugin/ directory. If the plugin's options are short, I keep them in a file called misc.lua, otherwise I create a separate file with the name of the plugin. Check out my config to see what I mean.