As far as I can tell, right now if you want to make customizations you have to edit data/user/init.lua inside your checkout of the lite repo. Most programs with similar config files allow you to store them as dotfiles in your home directory so you can keep it separate from the source for lite itself. Maybe something like ~/.config/lite/init.lua if you're on a unix system.

I can submit a patch for this if you think it's a good idea.