The difference is reported in their FAQ pages.
Pro Webmasters - Stack Exchange is for professional and enthusiast webmasters. If your question generally covers the operation of websites which you control, then you’re in the right place to ask your question!
If your question generally covers …
- Using Gmail, Facebook, Twitter, Google, or any other website which behaves like an application
- Browsers and their features relating to the use of a web application (Greasemonkey scripts for a web application, etc.)
… then you’re in the right place to ask your question!
In the first case, a question about the http.conf file for a website you control is on-topic on that site, but it would not be on-topic on Stack Overflow. In fact, Apache http.conf allow intranet was migrated there from Stack Overflow.
In the second case, a question about programming in Facebook would not be on-topic there, as questions there are about using Facebook, not creating a Facebook application, which would be on-topic on Stack Overflow.
Simplifying, the topics are:
Web servers you control
Web sites that works like desktop applications
Programming, and tools used from programmers