Hi, sorry for the lack of response, things have been busy for me specifically leading up to my wedding this weekend. We're also working on migrating our forums over to our new bbForums package which will help things stay much more organized.
Are you using WP 3.0 Beta? If so, the new menu system will let you add any links you want to your menus. Right now, the WP menu system in version prior to 3.0 are very restrictive and don't offer much customization. There are plugins out there that offer more functionality but with 3.0 so close to release - I'd say you should start to check it out.
You can also always add your Pod Pages as WordPress Pages in their specific spots on the site where you want them to appear. Pods will still run the pages as usual even if it's on the same URL as an existing WP Page or Post.