You need to create a plugin, render your template, and preRegister the result to the header template. Hook location parse_templates is a good one to use, and the code could be like:
Code:
$template = vB_Template::create('custom_header_mysite_beta');
$customheader = $template->render();
vB_Template::preRegister('header', array('custom_header_mysite_beta' => $customheader));