You have to have connectivity and the best way to do that is with a VPN. Assuming you have the VPN up and running then PHOENIX has to be configured to use a DNS server that is part of your domain and is Active Directory integrated so the zone for the domain has all the necessary information. PHOENIX should be configured to use AD DNS servers exclusively.
Suppose your domian is contoso.com. To test to see if your DNS is working correctly, open up a command prompt on PHOENIX and run
ping contoso.com. That should be resolved by DNS to one of your domain controllers. Since you only have ATLAS, it should be resolved to ATLAS and then ping. If you can succesfully ping the domain name from PHOENIX then you have 9/10 of the config you need and you might as well try joining PHOENIX at that point, since the other 1/10 is usually also working correctly.
If you're stuck on getting a VPN in place I would say that's another question, possibly for the Network Engineering Stack Exchange. A "hardware" or site-to-site VPN is best, unless you can swing a point-to-point link but that's going to be expensive for a non-profit. If you are 501(c)3 then check techsoup.org for Cisco hardware to terminate the VPN.