I need some help with what is probably a newbie question in terms of modifying phpBB.
I have a whole system developed in PHP, and I would like to integrate phpBB so
This is an old question so I'm sure you've worked something out by now, but if you need to refactor things in the future, this is entirely possible with authentication plugins in phpBB3:
http://wiki.phpbb.com/Authentication_plugins
I'm working on one now where phpBB is the "secondary" system, and it's going pretty well.