Forum Moderators: mack
There are TONS of discussions at the phpbb forums about how to do exactly this. Search their forums for phpbb logo and you'll find plenty of hints.
>I also want to add a spot for a rotating 486x60 ad banner at the top.
Just edit the include file yourphpbbboard/templates/subsilver/overall_header.tpl and include your own ad rotation code and change the phpbb logo. You can customize everey single part of your board through customizing the template files. Just look into your templates folder.
If you're firm with mysql / php, you might also have a look at the php files in your board's root folder as well as some include within your includes folder. You could add additional queries and display related content, news or other mods.