The scripts/helpers.sh file defines a lot of configurable options that can be set in one's .tmux.conf file. It would be nice to have exhaustive documentation of these in README.md.
For example, you can do set -g @yank_line 'C-y' in your .tmux.conf to change the yank-line keybinding from prefix + y to prefix + C-y. Currently this is undocumented.