The configuration for each package managed by dotfiles is stored in a directory. The directory structure for each package mimics the path the package expects its configuration file to be on the machine. For example, the shell expects a .zshrc file in the home directory so my .zshrc file is at dotfiles/zsh/.zshrc. For nvim which stores configs in ~/.config/nvim, the config files are at dotfiles/nvim/.config/<the_files>.
Run stow <package> and the config will get where it needs to be.
From use gnu stow to organize configuration files.
After initial install of yabai and skhd, run their respecitve startup commands:
yabai --start-service
skhd --start-serviceand then make sure they start at login and have whatever other accessibility permissions they require.