How to setup correctly a dns betwen hosting server and domain server?

Basicaly i have a server and i have a domain, i connect the domain with the server using masking which put the hosting inside of a iframe in the domain, but i will like to really connect the server with the domain so when you access the domain and every option in the website really show the domain site structure in where you are.

The thing is my server is hosting many websites, lets say the http://serverip/onewebsitefolder/ and so im redirecting onedomain.com to it but i dont know how to avoid the first paragraph problem.

The domain is manage by godaddy and the hosting in my own server.