two 'header' regions + primary nav alignment

Hello,
I apologize. I've uploaded the screen shots to our old site. Hopefully, this will work better.

1. Our logo is taller than the ST Conch logo, so the primary navigation gets floated to the top of the region, like so: http://www.ybboston.org/YBB-conch_header_1.jpg
2. I was was going to put the search-form in the upper right anyway, so I put it in the "header" region, thinking this might have a dual effect of helping push the navigation a bit lower. It does help push the navigation lower, but then I realized that the search form shows up twice: http://www.ybboston.org/YBB-conch_header_2.jpg
3. Looking in the admin/build/block interface, I realized that there are two regions called "header." I'm new to Drupal, so I'm not sure if this is normal. Could it be referencing two .info files? Duplicate code in page.tpl.php file? Heree's a screenshot of the interface: http://www.ybboston.org/YBB-conch_header_3.jpg
4. In the drop-down for selecting the block's placement, there is only one "header" option. It seems as though there must be some miscommunication, because I'm only selecting one "header" location, although the search box is being displayed twice. This shows the dropdown: http://www.ybboston.org/YBB-conch_header_4.jpg
5. I figured I'd just forget all this and place the search form in the "header-top" region instead. But I tried this, and it leaves too much empty/wasted space in the header. It also doesn't help push the primary navigation down closer to the slideshow. Here's what it looks like: http://www.ybboston.org/YBB-conch_header_5.jpg

So, is there an easy way to push the navigation to the bottom of its region? And is there a way to put the search box (or anything) in the header without it showing up twice?
Again, any help you can offer is greatly appreciated.