Using Htaccess/WebDAV

Hi - I wanted to password protect a directory on my webspace.

I have done it through the Web Control Panel > Goodies > Htaccess/WebDAV.

This has worked at stopping people access that directory but it has also stopped me uploading files to that dir via FTP.

I am using WS FTP - any ideas how I can get around this without having to go into the Control Panel and change it before I upload?

Thanks - Joe