It seems like you've got a mismatch between the directories allowed by your PHP open_basedir setting and the directories in your include_path.
If you can turn off open_basedir, that'd be the simplest solution, but you could also change your include_path to make sure it doesn't contain any directories that aren't also in open_basedir.
The warning you're getting from Omeka, way down the page, is because, while you set the permissions for the "archive" folder, you didn't set them for the folders inside "archive" (thumbnails, square_thumbnails, files, etc.).
Lastly, I see what looks like the default Apache page when I go to your domain root. That's to be expected if you've just installed omeka in the "omeka" subdirectory. If you want your domain root to go to your Omeka site, the easiest way would be to simply install Omeka in the document root, not a subdirectory named "omeka".