you'll have to explain a little more. Could you give an example of how you want to do it? Do you mean the html flashvars?
I would store a session in the php files, and then simply use php to handle the sessions. In flash you won't have to do anything (unless you want to check whether the user is logged in or not on every frame or something).
So basicly: you have to make a login form in the flash application (unless you allready log in via php), then check via php if the login information is correct, then store the information in a session. In flash you can check the sessions when necessary.
btw: if you're gonna use html flashvars, everyone will be able to see what you are passing to flash, and will be able to implement your swf, using the correct values of the flashvars.
UnrealEd