I have a client website that we developed and marketed for about a year and I ported all their pages to a dnn 6 installation. I am using GoDaddy as the hosting company. We have an unlimited shared hosting account. So I have my root folder, and under that all my domain folders, so we will say like this ...

root
domain1
domain2
domain3

I have 3 websites total and each of the domain folders has its own install of dnn, to keep my clients domains separate. My question and problem that is really bothering me is the clients domain name is pointing directly to the folder of domain1 and you land on www.domainname.com but anytime you search it displays the hosting folder www.domainname.com/domain1/home. So when I run my SEO programs to check my site content it thinks that every page is duplicated with itself with the hosting folder and without. I cannot have my client lose Google placement for some error such as this and in all my research that seems to happen. How can I make it so all my paths do not show the hosting folder. I have played with the alias settings but nothing seems to work.