Organising files

Hi

I am building a website which is bigger than ive done previouly with many different types of users.

In summary

There are public user who user the forum.
an administrator
And organisations user that can add events.

At the moment i am building object to support adding event and organisation. The forum will be provided by phpbb.

The question i have at the moment is what are the pros and con of running all the data through the index file or seperate files. Also there is the issue of where to use a templates or not.

I want to get the basic planning right so that i not going back on my self.

Ive been using pear to build forms for updating events.

I hope this not too broad.

Any planning advice would be good.