Hmmm, well I don't use GoDaddy and I know that perhaps their hosting accounts can be a pain in the butt. I know that many people register domain names through them, but usually have their sites hosted elsewhere. But, nonetheless, I believe Khenry, although I could be mistaken, but when I was testing out an install of Joomla, I was able to complete the whole installation right through Fantastico in Cpanel of my hosting account. I host my sites through
Vodahost, and register all my domains with Dynadot, but if you have Cpanel with your hosting it should be the same.
I also use Smart FTP but, all I can tell you on that is to make sure you have all of your information correct as far as which ftp account, your username and password etc. all being correct.
Hope that may help a bit anyhow!
Davin