WordPress Project

I am sure this is basically a dumb question that has been asked before but I could find it.

I am having not real issues installing WordPress, but I want to take some time in the custom design of it, and I currently have a html/php website already in place. I know I can’t install WordPress into the root because the index page will replace my current one, but when I installed WordPress in another directory to work on and attemted to move it to the root directory it no longer functioned. When I moved it back to the project directory it worked again, so the situation is obvious. Is there a way to work on designing the WordPress without losing your current website and beening down for a couple of weeks?