Hi Bryan,
It’s most likely because the header search is hard-coded to the theme, which makes it not replacable. There is a PHP shortcode for each search instance created: https://wpdreams.gitbooks.io/ajax-search-pro-documentation/content/getting_started/search_shortcode_in_themes.html
If you want, I can take a look at the theme source to see where to replace that. I can’t promise I can do it for you, as it qualifies as a customization request, but I can try of course. If so, I will need FTP access for that. Let me know!