.htaccess files can be placed at any directory level of a site so you can do it for just the subdomain or even just a directory of a domain.

Staging URL's are typically only used for testing so rather than do a deny I would recommend using a specific ALLOW for only the IP addresses that should be allowed access.

I would imagine you don't want it indexed because you don't want the rest of the world knowing about it.

You can also use HTACCESS to use username/passwords. It is simple but you can give that to clients if that is a concern/need.

Use an .htaccess file to only allow from certain ip addresses or ranges.

Here is an article describing how: http://www.kirupa.com/html5/htaccess_tricks.htm

I have placed the nav code at the bottom of the HTML doc at times. I can't really say that it is a significant difference for SEO. It doesn't take a lot of work to do if you are skilled with HTML/CSS but I can't really say that this methodology will have a long term benefit for SEO.

HTML 5 has new tags that sites should adopt such as

<nav>and other tags to indicate what that chunk of content is. These tags are supported by all major browsers at this point. I don't know all the specific browser versions. I would recommend this moving forward where possible. By using this tags the crawlers likely will not factor in position in the document to understand the importance of chunks of content.</nav>

The robots.txt file just tells the bots you would "prefer" they don't index but there is nothing to prevent them from indexing.The only sure way to do this is to restrict access to the sub-domain for everyone and require some sort of authentication. If they don't have access they can't index.

I personally use GoDaddy for purchasing domains but I do not use any of their add-ons. I would not recommend paying for their SEO tools. Submitting to any search engine is a free process and one that is easy to do.

For Bing go to: http://www.bing.com/toolbox/webmaster/

For Google go to: http://www.google.com/webmasters/

Setting up an account and doing so will also allow you to become familiar with their tools and reports that they provide. It is a great way to learn how and when they are indexing your site.

One additional thing to consider is to create a sitemap that dynamically gets updated as your site does. Submit this sitemap to the search engines and then it will improve the crawling efficiency and accuracy of the search engines. The individual responsible for your web development should be able to set this up for you.