I'm going to be paying to redo my site and I'm not going to be using the IIP or the sidebar anymore. I would still like to be able to adapt the PhotoPost featured photos pal into the header.php file (or footer.php perhaps). I don't however think I can just include the PHP statements from the pal box into the header.php file, or can I? I'm sure there is a way that this can be done, I just don't know how though. Is this possible?

yes. I attach as example my generic header. This one display a logo for each forum without generate for each forum a custom header. DB modification is needet for this example.