Yes, I changed my position to absolute because my logo img is rather large, and using this default Magento image function in the System–>Configuration–>Design will influence your layout. In my customized Hellococo template, my large logo pushed out my slider, which is a problem many people are having with HelloTheme templates. Don’t forget to edit your header.phtml file.
So you might need to position your logo with added CSS, so post your URL and I can help more. As far as SEO is concerned, you won’t have an image with an h1 tag, as you should really only have one h1 tag per page and it might be better used in an article title or something, although if you properly add the alt text to the image, you could just keep your h1 image tag.