iWeb itself is just software and it will continue to work. The only thing that Apple is discontinuing is hosting of websites, but as you're already using GoDaddy then there is nothing to do. So, I'm not sure what move you're referring to.
In any case, there are no tips or special tricks to uploading a website - it either works or not. In the case of the GoDaddy FTP tool it clearly failed to do its job, but Yummy is way more reliable than that.
