I had a bit of a tough time with this one. When setting up WP-DBPManger in a WordPress install on GoDaddy you will need to use different paths then what most of the forums are saying. The autodect feature in WP-DBManager does not work either when the provider is GoDaddy.
To get things working you will need to enter this info:
If you don’t have this info entered you will see red errors all over the place and the backup will not work properly.
Hope this helps anyone trying to setup WP-DBManager on GoDaddy!