I have also been using CNTLM for authenticating through our corporate proxy for installing npm packages, among other things. I'm currently writing up my experience using CNTLM and I won't go into it here but its pretty straight forward to install and configure.
If, like me you are already using CNTLM for npm then the .apmrc proxy configuration is the same as .npmrc proxy configuration. Basically, create the file C:\Users_username_.atom.apmrc and add your cntlm proxy details
This is how my .apmrc looks in my (now) working configuration.
My cntlm instance lives on my local host and listens on port 3128