Glad you got it squared away.
I don't use the actual dolphin admin banner part. I manually insert banners, images, ads and such. Since most of mine are google they rotate and change by themselves.
Then I just manually insert my google code something like
<center>
<script type="text/javascript"><!--
google_ad_client = "pub-xxxxxxxxxxxxx";
/* 728x15, created 11/2/08 */
google_ad_slot = "xxxxxxxxxxx";
google_ad_width = 728;
google_ad_height = 15;
//-->
</script>
<script type="text/javascript"
src="http://pagead2.googlesyndication.com/pagead/show_ads.js">
</script>
</center>
I just prefer to manually add the code myself rather than the __banner_top__ thing, but that is just me.
I also do the same for site logo. I don't use the admin panel, I manually insert it similarily. It just gives more control. And then I can positition it about anywhere using a html table.
_header.html and _footer.html will be available for all pages. You can also make some changes to say page_1.html which is the index.php / homepage and many of the other .html pages in the template folder.
Anyway it's just a matter of location and putting it in the right spot. You could just type some text like "test" refresh the page until you see "test" in the location you want the banner, then you know you are in the right spot.