functions, the best way to implement and arrange them..

It might be a simple question for the local die-hards among here, but i'm really wondering about how developers arrange their scripts and keep their map structures. today i was looking for the best way to keep my scripts clear and to put them into maps so i have a clear overview. the same thing i would do for the scripts, using the functions i have and throwing them in 1 or more php documents. i can not find it how it should be done. is it a good idea to put a couple of functions in just 1 document? like sessions and login/logout functions? in my idea i would only need to include a document in the header of my website and then i'm done, right? some thoughts, ideas and tips would be appreciated. kind regards taco