Adding a New WordPress Domain to a Subdirectory

Hi. This may be obvious, but I have a site that has one domain and wordpress-installed site in the main directory, and am planning on adding a second wordpress-installed site in a sub-directory. But eventually, I want this sub-directory site to overwrite the one in the main directory.

What changes do I make in the WordPress admin so that it will overwrite it, and still maintain links to the wordpress database. Specifically, where is it that I change the pathway???

Ellen