Today I made a rotating image on my website's header. I use Artisteer and changed the index.php and templateDetails.xml files to add a position 'header'. Then I installed an image rotator module which I got from extensions.joomla.org uploaded a folder with images the size of the header. Then I activated the image rotator module on the new 'header' position and instructed it where the images are. And this was all there was to it.
fun!

How does that affect the site's SEO if it is your header? I would imagine if both lots of code are appearing when the Google bot visits, then the tags are going to be the same and confuse Google re the relevance of each one. If the code only appears dependent on the header, then you could see fluctuations in rankings depending on which header was visible when the bot visited.

I think rotators should be left to sub levels where they are only images with alt tags relevant to the site's subject.

Justsayin'

Hi guys.
Where an element displays and where bots read it is not the same thing.
You can display the header images anywhere you want on the page using CSS and still have the bots read the content towards the top as opposed to lots of script needed for some of the pretty things.

I have had a similar SEO issues with site development and left/right columns, nav at top/bottom, etc. I had big issues with trying to achieve SEO/look/feel optimisation on some recent Magento projects, however we moved the the order of elements within the xml files and changed where they displayed with CSS.
This allowed us to change the order the content (text/code) is delivered to google, while achieving the look you desire.

I find that if you can use the CSS to drive where elements display, as opposed to changing other files, your SEO will be better. You can also try moving elements in other files further down the page, see if CSS keeps it where you want, but can display the most important content to the bots/google at the top of the page.

This would achieve a best (or better) outcome to meet recommendations of Ric and Ranger Hope this may assist is some peoples successful design and SEO results.