Unfortunately, if GoDaddy does not allow you to have access to below root folders, there's probably not much you can do other than change hosts.
Not to be negative, but from my experience and the general consensus from other developers I have worked with, GoDaddy is probably one of the worst places to host anything. They have a very cookie cutter approach with lack of customization and not great support either.
I know several hosts, though, that will allow you below root access and are probably even cheaper than GoDaddy. One that will allow you that access that I have found to have great customer support is Site5 www.site5.com/.