Note: I have a slightly older phpbb, but the permissions advice is generic.
Everyone does it their own way, but my advice is setup the forum permissions first and do it sensibly. This means use "all" and "reg" as much as possible and minimize the use of "private" except to those which must be set that way. The private means you manually assign groups - very tedious. By "sets it self up" I guess this refers to using the SIMPLE MODE? As to that, when configuring forum permissions do simple mode first for all forums then apply any "exceptions" in advanced mode.
Then when that's all setup, do your group permissions (which are based on the forum permissions) and only adjust the "exceptions" that remain, i.e. specific users who are admins/moderators.
If you have alot of forums with many groups, it will be complex, so reduce the groups to the bare min you need as best advice to streamline the entire process. Use rankings based in total replies to distinguish your best users, i.e. doesn't have to be done with groups unless you base access on performance.
I could have probably used less words to get these points across.
-jim