The layers do take a bit of time to get used to, but they become transparent, after a while. As for punctuation locations, I've exploited that to my advantage, I have brackets and braces (which I use a lot of, for Clojure) just next to my left ring and middle finger, and parenthesis are also trivially reachable, of course. (all this on a Dactyl Manuform, with 46 keys total)