http://qiita.com/takaeda/items/38ecf7d98d1a3ef99ef0 provides some guidance (in Japanese) and the modification that I've been dearly missing ever since Sierra broke Karabiner, which helps me preserve my linux/windows muscle memory by remapping left control to command except when the application is com.apple.Terminal, can be found here: https://pastebin.com/yY1NBUdS

(place cmd_to_ctrl_except_in_terminal.json in ~/.config/karabiner/assets/complex_modifications and add it as a rule in the Complex Modifications tab)