.jsbeautifyrcin your path with the options you want to set.
I want Atom Beautify to be the one-stop place for all code beautification in Atom. As of #282, each beautifier is very light-weight itself (e.g. https://github.com/Glavin001/atom-beautify/blob/master/src/beautifiers/autopep8.coffee ) and it'd be annoying for me to maintain at least (currently) 15 small repos for each beautifier, when right now they are simply files. So I am not supportive of splitting into separate modules, as the linter package does.
Essentially, I picture it as Atom Beautify being able to recognize each language it supports and then effectively install each module upon usage. Like linter package, except auto-installing: you do not need to install linter and then linter-coffeescript, you simply install linter and try to lint CoffeeScript and it will detect that it is supported and install it for you.