Pointing Domain to VDS Directory

I've got a domain name that is managed through 000Domains.com. I also have a virtual dedicated server hosted with GoDaddy.com. Within my VDS, I created a folder /mysite and placed all of my website files there. I can test this through the ipaddress of my VDS, but I would now like to point my domain from 000Domains over to my sub-directory hosted on GoDaddy. How do I do this? Do I need to make any specific modifications to my VDS to inform it that one of the directories will be accessible from a domain name?

I have access to Simple Control Panel, if that is of any relevance.

Update

I've used the [domains] portion of my Simple Control Panel to add my domain (mysite.com). Now it lists that domain name, and even gives me a nameserver for it, ns1.mysite.com. Still I know I need to some how point my hosted domain from 000Domains over to this Virtual Server. I'm not entirely sure how to do that though.

Update 2

Since adding the domain to my VDS (see Update 1), my ipaddress to the VDS goes directly to the directory that the server made for the domain. It made a directory other than the one I had been working in, but that's fine. When I added the domain name, I set it as a Master, so now the ipaddress for the server goes directly to that document root for this particular project. I have changed the A name on my domain registration to point to my VDS's ipaddress. It's been a few hours and it doesn't appear to be loading from the VDS yet.

Update 3

Well it's been several hours since I changed the A Name to the new VDS's ipaddress. Nothing yet has happened. The domain name with 000Domains still goes to the old server, and accessing the ipaddress of the VDS directly takes me to the new server.

When I changed the A Name on 000Domains.com, I was told that I must disable forwarding on the domain if the A Name were to function properly. I now have "disable forwarding" and "pass subdirectories" checked, but again, it's been around 12-15 hours with no hint of a change.