Installing WordPress Alongside Another Website

I am beginning to migrate my large website to WordPress one section at a time. Currently all of my sections are located in subdirectories (mysite.com/section), however with WordPress I am moving these to subdomains (section.mysite.com) using WordPress’s multisite feature.

I have one section running on WordPress ready to launch. What is the best way to put WordPress 3 onto my server so it will run conflict-free with the rest of my site?

The only conflicting filename is /httpdocs/index.php. If I change my current site’s DirectoryIndex to indexold.php, and run WordPress’s index.php file, will I still be able to access section.mysite.com while keeping the mysite.com/section files running while I continue migrating them? Will any of WordPress’s .htaccess declarations be problematic?