Customised too far?! Editing header to fit existing site

I’ve chosen Atitiude for a base for my blog, but I’m adding it to my existing website, so I’d been working on tweaking it to suit the header that the rest of the website uses.

It looks OK, but there’s a couple of issues! The important one, is that the css links have an active area that’s really deep, so clicking on a post at the top of the page actually activates a link!
basically my bodging of the css to get things to fit, means it’s in a right state!!

Does anyone know if there’s a simpler way of adding a whole chunk of html for a header (Same on every page), and letting WordPress just deal with the rest of the page?