Trying the best I can, I've been completely slammed at work and involved in a new startup.
If there's a layout.tpl file, then it will ignore the header.tpl/footer.tpl. Docs here:
http://forum.phpvms.net/page/index.html/_/skinning-and-customization-guides/skin-elements-r20
I mean, start small, and use that example in the docs there. You'll have problems going to some uber complex layout directly without starting really small and seeing how it works. As for tutorials, they're down because they're all old and have stuff from 1.0 in them. I haven't had the time to record, and I don't have a mic either. But yes, if someone can whip up a quick tutorial, that'd be great