Here is what they forget to tell you at godaddy. On Windows hosting you can host multiple sites but you won’t be able to see each individual site on the management area or when you install WP. You have to be on their linux hosting to see each individual site as it’s own domain.
Here is one way I have heard to get around this.
I have several names registered.
A.com
B.com
C.com
Let a name you don’t care about be C
set it up as your primary domain which will have the \ root directory
create a folder called A point A.com to this folder
and a folder called B point B.com to this folder
Now when you install WP only C.com will be visible if you are dealing with a windows host
choose that domain and then install into the appropriate folder A or B
I have yet to try the second install but I have read it works, I am about to do so therefore if I have trouble I will come back and update.
HTH
Tony