I have not done this with ZenCart either but it should be able to be accomplished and maybe without touching tany of the php stuff.

The Zen method for this(header& other elements)is that they define in css a wrapper and then the content. Having seen what the wrapper does and how it emulates a table, you might have to strip the wrapper for the header and check the php header files to see if they reference the wrapper. And define and position your header another way along with any other items that you will use from the zencart layot.

the z-index hierarchy should work then. You will just have to separate and maybe redefine the centerbox for the mainpage vs the other pages. I would create another for the main and let Zen use centerbox for the rest.