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The SQL code won't be sent to the browser, but rather executed server side, so is doesn't matter where it is in the page except that it has to be before the part of the page where you output the results.
However after saying that, it gives you more flexability if you place it before the <html> or any other Response as you can then do tricks like issuing a 301 or 302 redirect if necessary and this needs to occur before you actually start sending any other response to the browser.
How is it being indexed, and what is the problem you are encountering?
Search engines don't know what you are doing with SQL statements, they only read HTML.
Some people have described a sandbox effect with Google, in that domains that are newly registered won't appear in Google's indexes for up to six months.
Other people deny that this exists. I've never seen a statement from Google on the matter.
The only thing you can do is see if you can get more inbound links from other sites, and eventually you will appear in Google.
Do a search for Google Sandbox and you will find a lot of talk on this subject.
