In the current version the most important settings are mapped in the administration panel. The WP Flash Uploader uses the TWG Flash Uploader which has much more features that can be directly configured here. If you want to configure WFU in more detail you can edit the tfu_config.php directly.
2 configuration files do exists: tfu_config.php and my_tfu_config.php. They are in the directory wp-content/plugins/wp-flash-uploader/tfu.
my_tfu_config.php is the configuration file that sets all settings you can set in WordPress and does overwrite the settings in tfu_config.php.
Check tfu_config.php to see al the available settings you can make. There are around 80 ;). If you make any changes always check in my_tfu_config.php if they are not overwritten. I have connected some of them to make configuration in WordPress easier.
Since 2.16 this is even more flexible. Please read the advanced section in the plugin! There is a lot of documentation.
If you need more help fee free to post it in the forum.