To use an alternate directory for publishing your assets, you simply need to do these two steps:
1)Ensure the directory you wish to publish to exists and is writable by the web application.
2) Add a configuration entry for the assetManager in your main config file within the components section:
'assetManager'=>array( 'basePath'=>'fullbasepath'.DIRECTORY_SEPARATOR.'alternateDirectoryName', 'baseUrl'=>DIRECTORY_SEPARATOR.'alternateDirectoryName', ),
That's it. I had found the basePath pretty early on, but I didn't realize that you need to alter the publishing path AND the url to keep them pointed to the same location. It doesn't do that automatically. ;)