Unzip the downloaded package and upload the flexible-upload folder into the wp-content/plugins/ directory
Log into your WordPress admin panel
Activate the plugin through the 'Plugins' menu in WordPress (if you are upgrading from an earlier version, make sure to de-activate and re-activate the plugin so that all options are updated)
Be sure to check the option page (available from the 'Options' > 'Flexible Upload' menu)
A detailed explanation of each feature is available in the local help page (link at the top of the option page)