Go into the Domain Name Service Manager option your Member's Area and enter the nameserver information that was provided with your hosting. If you can't find the nameserver info then you will have to raise a support ticket to ask Bravenet staff.
If bravenet is where I got the domain and it doing the "free" hosting, do I still have to transfer files from my bravenet.com site to my new.domain.com site or will transfer automatically?
Even though you manage them from the same Account Manager, your domain name and your web hosting are really separate issues. In your case, there is nothing to transfer. You set the name servers from your domain name manager and Bravenet will take care of making sure it points to your site correctly.
