You need to understand Wordpress structure can be confusing at first but you will fall in love with it once you figure it out.
This is a site that should absolutely be in your bookmarks:
Wordpress is considered a blog or CMS platform, basically meaning you are going to have to customize your design as a template to work with Wordpress.
If you want to just have a subdomain for your Wordpress installation you can do that without any problems.
So wordpress would be http://blog.mydomain.com
is your custom site.
Like i said above you only option with Wordpress is to use a template someone else made or customize your own to work with Wordpress.