I'm not sure what Flex is, what it's written in, and where it runs (remotely to the classes or locally, on the same process or not).
If Flex is a php script/framework and uses the classes as regular php classeses, you don't need to perform any special actions. Just start debugging Flex and all breakpoints you have in the classes will trigger. If you want, you may uncheck "stop on the first line after run" in the debugger settings.
If Flex is a service that runs the classes through a protocol like HTTP or SOAP, you need a way to inform the classes' side that you want to debug them. It can be done with may ways described there
http://forum.nusphere.com/howto-run-debug-session-t585.html
Finally, as a last resort, you can put "hardcoded" breakpoint into your code. It can be done with DebugBreak() function call.