What are the best practices for changing my page structure and skin without causing the users any distruption? Is there any documentation for this procedure when using DotNetNuke?

This is going to depend on the degree to which the site needs a reorganizing.

I would start by making a copy of your site and installing it locally. Then, you can install the new skin and test it. You can also make any necessary changes to your pages and page structure and organization. Once you have everything set, you can replace the existing site with your offline version.

This will result in some downtime. Schedule the maintenance for a time that the site is less busy.

If you must absolutely minimize downtime, you could install the altered site in parallel with the live one. Then, at the time you are ready to switch, change IIS and/or portal aliases to make the changed site the live one.

Don't use SQL, use the classes and methods provided by the framework. Use the UserInfo object in the framework. You find the user's profile there and, in it, Country.