What is the difference between the two sites? Doesn't Stack Overflow cover Facebook programming topics? Why is it a separate site instead of just using a facebook tag on the regular Stack Overflow site?
Facebook.SO is not a separate site. It's just a subdomain sponsored by Facebook. All it does is display questions which are tagged with facebook.
WebApps.SE is a separate site for web applications for end users, which would cover most Facebook end user questions that are not covered by Stack Overflow's programming question policy.