Hi,
You're (poissibly) going to run into permissions issues when it comes to file uploads. suPHP is nice because the upload directory can be owned by the user with more restrictive permissions than DSO. When running DSO, the upload directory needs to be owned by 'nobody' or have 777 permissions in order for PHP to save uploaded files to it.
Also, if you've created a custom php.ini file in any account to modify global PHP settings, you'll need to add your modified settings to .htaccess as "php_value" directives, as DSO doesn't check for local php.ini files.