Which database are you referring to? Databases should not be in the domain folder or any sub folders within it. Create a separate DB folder in the root
Hmm, actually you should enable either raw logs, or use Webalizer to see if search engine hits your site.
I'm not quite sure, but as I remember right, robots.txt is used to tell to search bot what to index and what not. At least this is what I'm using it for