As long as you're using Friendly URLs, you should be able to rename the index.php file and edit the .htaccess file to use newindex.php instead of index.php in the rewrite rules
# For Friendly URLs
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule ^(.*)$ newindex.php?q=$1 [L,QSA]
However, I don't think this will be any help for running it alongside your existing site, as it will be trying to serve every page requested through MODx. You really need to have either your MODx installation in a subfolder, or move the existing site into a subfolder.
If you don't use friendly URLs, then MODx must have index.php, as that's what it uses internally to generate URLs.
[ed. note: sottwell last edited this post 14 years, 5 months ago.]